X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2W1YPDB ENTRY 2W1Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH6.5277HEWL co-crystallized with cisplatin in 462.5 uL 0.05 M sodium acetate, pH 6.5, 462.5 uL 10% sodium chloride, and 75 uL DMSO, BATCH, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0539.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.641α = 90
b = 79.641β = 90
c = 37.018γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVOsmic Confocal Max-Flux, blue configuration2011-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
12.530.9454.70.13622.624.63234177242
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)
12.52.5897.30.5286.124.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)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 2W1Y328.1624323417727370.10.216840.213990.2795RANDOM17.811
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]
0.220.22-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.751
r_dihedral_angle_3_deg16.27
r_dihedral_angle_4_deg14.599
r_dihedral_angle_1_deg6.001
r_angle_other_deg2.223
r_angle_refined_deg1.173
r_chiral_restr0.064
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.751
r_dihedral_angle_3_deg16.27
r_dihedral_angle_4_deg14.599
r_dihedral_angle_1_deg6.001
r_angle_other_deg2.223
r_angle_refined_deg1.173
r_chiral_restr0.064
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms31
Heterogen Atoms48

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
EVAL15data reduction
EVAL15data scaling