4YEM

Carboplatin binding to HEWL in NaBr crystallisation conditions studied at an X-ray wavelength of 0.9163A - new refinement


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XAN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE4.7297co-crystallizing 20 mg ml HEWL with 1.4 mg carboplatin in 75 ml DMSO, 462.5 ml 0.1 M sodium acetate, 462.5 ml 1 M NaBr solution.
Crystal Properties
Matthews coefficientSolvent content
2.0138.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.58α = 90
b = 78.58β = 90
c = 37.29γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9163DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.4755.5694.60.090.0916.310.618627176724212.3
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)
11.471.5640.464.28.9

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4XAN1.4739.291767293391.010.10770.10530.1559RANDOM14.86
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]
-0.1-0.10.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.302
r_sphericity_free25.729
r_dihedral_angle_4_deg20.293
r_dihedral_angle_3_deg13.444
r_sphericity_bonded10.609
r_dihedral_angle_1_deg5.846
r_angle_other_deg1.923
r_rigid_bond_restr1.871
r_mcangle_it1.51
r_angle_refined_deg1.494
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.302
r_sphericity_free25.729
r_dihedral_angle_4_deg20.293
r_dihedral_angle_3_deg13.444
r_sphericity_bonded10.609
r_dihedral_angle_1_deg5.846
r_angle_other_deg1.923
r_rigid_bond_restr1.871
r_mcangle_it1.51
r_angle_refined_deg1.494
r_mcbond_it1.237
r_mcbond_other1.188
r_chiral_restr0.113
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_gen_planes_other0.006
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms182
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
MOSFLMdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing