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X-ray Structure of the Adduct formed between cisplatin and Ribonuclease A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JVT PDB code 1JVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 Crystals of RNase A were grown by hanging-drop vapor diffusion technique at 298 K mixing a protein solution containing 20 mg mL-1 of RNase A with equal volumes of reservoir solution. Well diffracting crystals appeared within 15days from the following conditions:20% PEG4000 and 20 mM sodium citrate buffer pH 5.0. , VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 1.99 38.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.767 α = 90 b = 32.463 β = 93.07 c = 67.575 γ = 90
Symmetry Space Group C 1 2 1
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 RIGAKU SATURN 944+ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 50 17075 17075
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 code 1JVT 1.85 30.88 16195 16195 880 91.12 0.192 0.19235 0.18924 0.198 0.24709 0.2499 RANDOM 27.794
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] 0.03 0.24 0.82 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.309 r_dihedral_angle_4_deg 17.15 r_dihedral_angle_3_deg 13.064 r_dihedral_angle_1_deg 8.582 r_long_range_B_other 8.194 r_long_range_B_refined 8.161 r_mcangle_it 4.378 r_mcangle_other 4.376 r_scangle_other 4.235 r_mcbond_other 2.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.309 r_dihedral_angle_4_deg 17.15 r_dihedral_angle_3_deg 13.064 r_dihedral_angle_1_deg 8.582 r_long_range_B_other 8.194 r_long_range_B_refined 8.161 r_mcangle_it 4.378 r_mcangle_other 4.376 r_scangle_other 4.235 r_mcbond_other 2.814 r_mcbond_it 2.813 r_scbond_it 2.802 r_scbond_other 2.802 r_angle_refined_deg 1.799 r_angle_other_deg 0.913 r_chiral_restr 0.115 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1851 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 8
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling