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Crystal structure of cisplatin bound to a human copper chaperone (dimer) - new refinement
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IWX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 1.5 M LITHIUM SULFATE, 0.1M MES, 50 MM NACL, PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 3.24 62.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.289 α = 90 b = 78.289 β = 90 c = 54.335 γ = 120
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 21-ID-F 0.97872 APS 21-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.14 50 99.9 0.078 0.078 23.4 5.6 10562 33.3
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 2.14 2.18 100 0.401 3.5 5.5
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 3iwx 2.14 25.63 10030 503 99.82 0.1621 0.1602 0.1667 0.1974 0.2079 RANDOM 36.165
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] 0.1 0.05 0.1 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.285 r_sphericity_bonded 17.818 r_dihedral_angle_3_deg 12.75 r_dihedral_angle_4_deg 7.048 r_dihedral_angle_1_deg 6.937 r_angle_refined_deg 1.469 r_mcangle_it 1.015 r_angle_other_deg 0.884 r_mcbond_it 0.627 r_mcbond_other 0.624
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.285 r_sphericity_bonded 17.818 r_dihedral_angle_3_deg 12.75 r_dihedral_angle_4_deg 7.048 r_dihedral_angle_1_deg 6.937 r_angle_refined_deg 1.469 r_mcangle_it 1.015 r_angle_other_deg 0.884 r_mcbond_it 0.627 r_mcbond_other 0.624 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1012 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building