1Z53
The 1.13 Angstrom Structure of Iron-free Cytochrome c Peroxidase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 277 | 30% 2-methyl-2,4-pentanediol (MPD), 50 mM Tris-phosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.67 | 53.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 106.852 | α = 90 |
b = 75.736 | β = 90 |
c = 51.041 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 116 | IMAGE PLATE | MARRESEARCH | mirrors | 2003-02-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-1 | 0.78 | SSRL | BL9-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 1.13 | 100 | 98.5 | 0.061 | 27 | 8.625 | 189599 | 189599 | 2 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.13 | 1.16 | 97.9 | 0.48 | 2.55 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | AB INITIO PHASING | FREE R | Atomic resolution structure of Wild Type CcP | 1.13 | 10 | 153609 | 148486 | 5123 | 95.9 | 0.134 | 0.1471 | 0.1471 | 0.1773 | RANDOM |
Coordinate Error | ||
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Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
16 | 2223.1 | 2935.4 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_non_zero_chiral_vol | 0.098 |
s_zero_chiral_vol | 0.089 |
s_anti_bump_dis_restr | 0.069 |
s_similar_adp_cmpnt | 0.051 |
s_angle_d | 0.03 |
s_from_restr_planes | 0.0283 |
s_bond_d | 0.015 |
s_rigid_bond_adp_cmpnt | 0.005 |
s_similar_dist | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2449 |
Nucleic Acid Atoms | |
Solvent Atoms | 530 |
Heterogen Atoms | 42 |
Software
Software | |
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Software Name | Purpose |
SHELX | model building |
SHELXL-97 | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
SHELX | phasing |