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100K X-ray diffraction study of carboplatin binding to HEWL in DMSO media after 13 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 49 mg HEWL co-crystallized with 3.7 mg carboplatin in 462.5 uL 0.04 M sodium acetate + 462.5 uL 10% sodium chloride + 75 uL DMSO, pH 4.7, BATCH, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.91 35.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.177 α = 90 b = 77.177 β = 90 c = 36.709 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 100 CCD APEX II CCD Incoatec Helios confocal optics 2012-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 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 54.573 52 0.163 18.5 28.6 14368 7533 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 2.04 100 0.657 4.8 13.6 472
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2W1Y 2 54.573 2 4 14368 7533 363 99.66 0.20819 0.20538 0.2142 0.26829 0.2729 RANDOM 17.954
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] -0.43 -0.43 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.295 r_dihedral_angle_4_deg 19.578 r_dihedral_angle_3_deg 15.042 r_dihedral_angle_1_deg 6.783 r_angle_refined_deg 1.793 r_angle_other_deg 1.095 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.295 r_dihedral_angle_4_deg 19.578 r_dihedral_angle_3_deg 15.042 r_dihedral_angle_1_deg 6.783 r_angle_refined_deg 1.793 r_angle_other_deg 1.095 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.004 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 37 Heterogen Atoms 21
Software Software Software Name Purpose APEX data collection PHASER phasing REFMAC refinement EVAL15 data reduction EVAL15 data scaling