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HEWL co-crystallization with cisplatin in DMSO media with glycerol as the cryoprotectant
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 + 3 mg cisplatin in 462.5 uL 0.04 M sodium acetate + 75 uL DMSO + 462.5 uL 10% sodium chloride, with glycerol as cryoprotectant, pH 4.7, BATCH, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.98 38.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.443 α = 90 b = 78.443 β = 90 c = 36.971 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 Bruker Platinum 135 Incoatec Helios confocal optics 2011-02-17 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) 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 1.69 55.47 92.6 0.037 0.037 20.8 13.11 13407 12148 4 2 20.8
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 1.69 1.79 75.2 0.155 7.82 5.96 13704
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 (All) 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 1.69 55.47 2 4 13407 12148 623 95.26 0.2088 0.17858 0.17523 0.2145 0.24857 0.2684 RANDOM 23.617
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 38.365 r_dihedral_angle_4_deg 14.948 r_dihedral_angle_3_deg 13.023 r_dihedral_angle_1_deg 6.774 r_scangle_it 4.63 r_scbond_it 3.162 r_angle_refined_deg 2.071 r_mcangle_it 1.877 r_mcbond_it 1.278 r_chiral_restr 0.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.365 r_dihedral_angle_4_deg 14.948 r_dihedral_angle_3_deg 13.023 r_dihedral_angle_1_deg 6.774 r_scangle_it 4.63 r_scbond_it 3.162 r_angle_refined_deg 2.071 r_mcangle_it 1.877 r_mcbond_it 1.278 r_chiral_restr 0.171 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 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 107 Heterogen Atoms 201
Software Software Software Name Purpose PROTEUM PLUS data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling