X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH4.7277HEWL co-crystallized with cisplatin and N-acetylglucosamine in 462.5 uL 0.05 M sodium acetate and 462.5 uL 10% sodium chloride in 75 uL DMSO, pH 4.7, BATCH, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.9938.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.949α = 90
b = 79.089β = 90
c = 36.984γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135Incoatec Helios confocal optics2011-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
11.879.08994.60.07922.915.1219492184342
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)
11.81.8695.20.2134.25.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 2W1Y1.819.172188420721112099.760.220970.219290.25296RANDOM16.387
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.639
r_dihedral_angle_3_deg14.357
r_dihedral_angle_4_deg13.129
r_dihedral_angle_1_deg6.427
r_angle_refined_deg1.805
r_angle_other_deg1.236
r_chiral_restr0.114
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.639
r_dihedral_angle_3_deg14.357
r_dihedral_angle_4_deg13.129
r_dihedral_angle_1_deg6.427
r_angle_refined_deg1.805
r_angle_other_deg1.236
r_chiral_restr0.114
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.005
r_gen_planes_other0.004
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 Atoms2002
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms49

Software

Software
Software NamePurpose
PROTEUM PLUSdata collection
PHASERphasing
REFMACrefinement
EVAL15data reduction
EVAL15data scaling