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Crystal structure of cisplatin bound to a human copper chaperone (monomer) - new refinement
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IWL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 2M lithium sulfate, 0.1M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.22 61.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.07 α = 90 b = 54.07 β = 90 c = 55.578 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 CCD MARRESEARCH 2009-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.90511 APS 23-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.6 50 99.7 0.118 0.118 24.9 19.5 13182 -3 17.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 99.7 0.503 3.3 9.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 3iwl 1.602 27.03 12057 621 99.54 0.1369 0.136 0.1357 0.1555 0.1542 RANDOM 22.116
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] 0.09 0.05 0.09 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.156 r_sphericity_bonded 14.689 r_dihedral_angle_3_deg 11.505 r_dihedral_angle_4_deg 11.24 r_dihedral_angle_1_deg 5.603 r_rigid_bond_restr 1.572 r_angle_refined_deg 1.515 r_angle_other_deg 0.913 r_mcangle_it 0.812 r_mcbond_it 0.487
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.156 r_sphericity_bonded 14.689 r_dihedral_angle_3_deg 11.505 r_dihedral_angle_4_deg 11.24 r_dihedral_angle_1_deg 5.603 r_rigid_bond_restr 1.572 r_angle_refined_deg 1.515 r_angle_other_deg 0.913 r_mcangle_it 0.812 r_mcbond_it 0.487 r_mcbond_other 0.462 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 503 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing SHARP phasing Coot model building HKL-2000 data scaling