4YEA

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62941.5 M LITHIUM SULFATE, 0.1M MES, 50 MM NACL, PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K
Crystal Properties
Matthews coefficientSolvent content
3.2462.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.289α = 90
b = 78.289β = 90
c = 54.335γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDMARRESEARCH2009-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
12.145099.90.0780.07823.45.61056233.3
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)
12.142.181000.4013.55.5

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 SYNTHESISTHROUGHOUT3iwx2.1425.631003050399.820.16210.16020.1974RANDOM36.165
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]
0.10.050.1-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.285
r_sphericity_bonded17.818
r_dihedral_angle_3_deg12.75
r_dihedral_angle_4_deg7.048
r_dihedral_angle_1_deg6.937
r_angle_refined_deg1.469
r_mcangle_it1.015
r_angle_other_deg0.884
r_mcbond_it0.627
r_mcbond_other0.624
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.285
r_sphericity_bonded17.818
r_dihedral_angle_3_deg12.75
r_dihedral_angle_4_deg7.048
r_dihedral_angle_1_deg6.937
r_angle_refined_deg1.469
r_mcangle_it1.015
r_angle_other_deg0.884
r_mcbond_it0.627
r_mcbond_other0.624
r_chiral_restr0.082
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1012
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms16

Software

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