4G4H

100K X-ray diffraction study of carboplatin binding to HEWL in DMSO media after 13 months of crystal storage


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH4.729549 mg HEWL co-crystallized with 3.7 mg carboplatin in 462.5 uL 0.04 M sodium acetate + 462.5 uL 10% sodium chloride + 75 uL DMSO, pH 4.7, BATCH, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9135.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.177α = 90
b = 77.177β = 90
c = 36.709γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAPEX II CCDIncoatec Helios confocal optics2012-05-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR-H1.5418

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
1254.573520.16318.528.614368753342
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)
122.041000.6574.813.6472

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 2W1Y254.5732414368753336399.660.208190.205380.26829RANDOM17.954
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]
-0.43-0.430.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.295
r_dihedral_angle_4_deg19.578
r_dihedral_angle_3_deg15.042
r_dihedral_angle_1_deg6.783
r_angle_refined_deg1.793
r_angle_other_deg1.095
r_chiral_restr0.112
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.295
r_dihedral_angle_4_deg19.578
r_dihedral_angle_3_deg15.042
r_dihedral_angle_1_deg6.783
r_angle_refined_deg1.793
r_angle_other_deg1.095
r_chiral_restr0.112
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.001
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 Atoms37
Heterogen Atoms21

Software

Software
Software NamePurpose
APEXdata collection
PHASERphasing
REFMACrefinement
EVAL15data reduction
EVAL15data scaling