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HEWL co-crystallization with cisplatin in DMSO media with paratone as the cryoprotectant at pH 6.5
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 6.5 277 20 mg HEWL + 1.1 mg cisplatin in 462.5 uL 0.04 M sodium acetate + 75 uL DMSO + 462.5 uL 10% sodium chloride, with paratone as cryoprotectant, pH 6.5, BATCH, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.04 39.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.46 α = 90 b = 79.46 β = 90 c = 36.96 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 IMAGE PLATE RIGAKU RAXIS IV Osmic Confocal Max-Flux, blue configuration 2011-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 3 56.19 56.9 0.15 0.15 5.8 3.18 4150 2365 4 2 27.9
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 3 3.11 91.3 0.226 3.2 3.15 4150
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 3 33.51 2 4 4150 2365 109 94.54 0.2136 0.21141 0.2188 0.25852 0.2726 RANDOM 42.113
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.853 r_dihedral_angle_4_deg 21.234 r_dihedral_angle_3_deg 20.305 r_dihedral_angle_1_deg 7.208 r_scangle_it 2.181 r_angle_refined_deg 1.691 r_scbond_it 1.301 r_mcangle_it 0.795 r_mcbond_it 0.405 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.853 r_dihedral_angle_4_deg 21.234 r_dihedral_angle_3_deg 20.305 r_dihedral_angle_1_deg 7.208 r_scangle_it 2.181 r_angle_refined_deg 1.691 r_scbond_it 1.301 r_mcangle_it 0.795 r_mcbond_it 0.405 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other 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 7 Heterogen Atoms 30
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling