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Room temperature X-ray diffraction of cisplatin binding to HEWL in aqueous media after 15 months of crystal storage
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W1Y PDB ENTRY 2W1Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH 4.7 295 HEWL co-crystallized with cisplatin in 1 mL 10% sodium chloride + 1 ml 0.04 M sodium acetate, pH 4.7, BATCH, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.06 40.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.671 α = 90 b = 78.671 β = 90 c = 38.068 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 CCD APEX II CCD 2012-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.4 55.629 50 0.151 13.7 10.8 8952 4770 4 2
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 2.4 2.44 100 0.623 3.9 8.9 283
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MIR THROUGHOUT PDB ENTRY 2W1Y 2.4 55.629 2 4 8952 4770 233 99.9 0.1773 0.17563 0.1837 0.20955 0.207 RANDOM 35.371
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] -0.49 -0.49 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.56 r_dihedral_angle_4_deg 18.703 r_dihedral_angle_3_deg 15.778 r_dihedral_angle_1_deg 6.285 r_angle_refined_deg 1.417 r_angle_other_deg 0.949 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.56 r_dihedral_angle_4_deg 18.703 r_dihedral_angle_3_deg 15.778 r_dihedral_angle_1_deg 6.285 r_angle_refined_deg 1.417 r_angle_other_deg 0.949 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 13
Software Software Software Name Purpose APEX data collection PHASER phasing REFMAC refinement EVAL15 data reduction EVAL15 data scaling