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Carboplatin binding to HEWL in 2M NH4formate, 0.1M HEPES at pH 7.5
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 VAPOR DIFFUSION, HANGING DROP 7.5 298 20mg of HEWL (0.6mM) was dissolved in 1ml distilled water. 1.4mg of carboplatin (1.8mM) was added with 75 l DMSO. 2 l of this was mixed with 2 l of resevoir solution 2M NH4formate, 0.1M HEPES at pH 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.94 36.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.496 α = 90 b = 77.496 β = 90 c = 37.123 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 2013-08-08 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 1.7 33.5 94.7 0.212 19.3 63.5 13055 12367 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 1.7 1.8 98.7 0.942 1.4 30.1
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 SAD THROUGHOUT PDB ENTRY 2W1Y 1.7 33.5 2 4 13055 12367 632 99.59 0.201 0.20189 0.1992 0.2064 0.25757 0.2647 RANDOM 19.237
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] -0.14 -0.14 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.772 r_dihedral_angle_4_deg 20.572 r_dihedral_angle_3_deg 15.837 r_long_range_B_refined 6.867 r_dihedral_angle_1_deg 6.337 r_scbond_it 3.071 r_mcangle_it 2.365 r_angle_refined_deg 2.156 r_mcbond_it 1.635 r_chiral_restr 0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.772 r_dihedral_angle_4_deg 20.572 r_dihedral_angle_3_deg 15.837 r_long_range_B_refined 6.867 r_dihedral_angle_1_deg 6.337 r_scbond_it 3.071 r_mcangle_it 2.365 r_angle_refined_deg 2.156 r_mcbond_it 1.635 r_chiral_restr 0.131 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_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 61 Heterogen Atoms 74
Software Software Software Name Purpose APEX data collection PHASER phasing REFMAC refinement SAINT data reduction APEX data reduction