2V3I

Hypocrea jecorina Cel7A in complex with (R)-dihydroxy-phenanthrenolol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DY4PDB ENTRY 1DY4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5298POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, GLYCEROL, COBALT CHLORIDE, SODIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298 K
Crystal Properties
Matthews coefficientSolvent content
239

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.957α = 90
b = 82.934β = 90
c = 110.659γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2006-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.0526.899.20.1118.19.61748832
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)
11.051.07900.365.36.2

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1DY41.0526.82166415880899.20.120.1190.14RANDOM14.83
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]
0.02-0.060.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.197
r_dihedral_angle_4_deg16.494
r_dihedral_angle_3_deg10.905
r_dihedral_angle_1_deg6.575
r_scangle_it4.604
r_scbond_it3.442
r_mcangle_it3.272
r_mcbond_it2.385
r_angle_refined_deg1.771
r_symmetry_vdw_refined0.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.197
r_dihedral_angle_4_deg16.494
r_dihedral_angle_3_deg10.905
r_dihedral_angle_1_deg6.575
r_scangle_it4.604
r_scbond_it3.442
r_mcangle_it3.272
r_mcbond_it2.385
r_angle_refined_deg1.771
r_symmetry_vdw_refined0.318
r_nbtor_refined0.306
r_nbd_refined0.21
r_symmetry_hbond_refined0.208
r_xyhbond_nbd_refined0.16
r_chiral_restr0.11
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3220
Nucleic Acid Atoms
Solvent Atoms700
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing