4YDX

Crystal structure of cisplatin bound to a human copper chaperone (monomer) - new refinement


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IWL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62942M lithium sulfate, 0.1M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.2261.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.07α = 90
b = 54.07β = 90
c = 55.578γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDMARRESEARCH2009-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.90511APS23-ID-B

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
11.65099.70.1180.11824.919.513182-317.5
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)
11.61.6399.70.5033.39.5

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 SYNTHESISTHROUGHOUT3iwl1.60227.031205762199.540.13690.1360.1555RANDOM22.116
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]
0.090.050.09-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.156
r_sphericity_bonded14.689
r_dihedral_angle_3_deg11.505
r_dihedral_angle_4_deg11.24
r_dihedral_angle_1_deg5.603
r_rigid_bond_restr1.572
r_angle_refined_deg1.515
r_angle_other_deg0.913
r_mcangle_it0.812
r_mcbond_it0.487
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.156
r_sphericity_bonded14.689
r_dihedral_angle_3_deg11.505
r_dihedral_angle_4_deg11.24
r_dihedral_angle_1_deg5.603
r_rigid_bond_restr1.572
r_angle_refined_deg1.515
r_angle_other_deg0.913
r_mcangle_it0.812
r_mcbond_it0.487
r_mcbond_other0.462
r_chiral_restr0.093
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms503
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
SHARPphasing
Cootmodel building
HKL-2000data scaling