5CVQ

Structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv oryzae, in complex with actinonin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5E5D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52870.05M Cadmium sulfate, 0.1M HEPES, 2.0M Sodium acetate trihydrate, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
3.4564.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.641α = 90
b = 58.641β = 90
c = 265.848γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102009-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 4A0.99PAL/PLS4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.25093.59.26.613892
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.291.60.6722.16.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5E5D2.527.84922647194.960.174060.171830.170.218220.22RANDOM26.069
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.659
r_dihedral_angle_4_deg19.518
r_dihedral_angle_3_deg14.134
r_dihedral_angle_1_deg7.238
r_long_range_B_refined6.064
r_scbond_it3.11
r_mcangle_it2.668
r_angle_refined_deg1.992
r_mcbond_it1.794
r_chiral_restr0.132
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1230
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing