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The X-ray structure of the adduct formed in the reaction between bovine pancreatic ribonuclease and arsenoplatin-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.1 298 22% w/v PEG4K, 10 mM sodium acetate pH 5.1. Crystals of RNase A-AP-1 were formed by soaking pre-grown RNase A crystals for 3 h in a solution containing 5 mM AP-1 dissolved in DMSO and then added to the reservoir.
Crystal Properties Matthews coefficient Solvent content 2.2 44.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.535 α = 90 b = 32.855 β = 90.17 c = 72.939 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 mirrors 2014-10-09 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) 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 2.15 72.94 99.7 0.117 10 3.4 13274
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1JVT 2.15 72.94 12526 681 99.5 0.1904 0.18704 0.1927 0.25049 0.2541 RANDOM 33.698
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] -1.33 -0.19 0.16 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.616 r_dihedral_angle_3_deg 14.759 r_dihedral_angle_4_deg 13.999 r_dihedral_angle_1_deg 7.077 r_long_range_B_refined 7.023 r_long_range_B_other 6.784 r_scangle_other 4.444 r_mcangle_other 4.155 r_mcangle_it 4.154 r_scbond_it 3.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.616 r_dihedral_angle_3_deg 14.759 r_dihedral_angle_4_deg 13.999 r_dihedral_angle_1_deg 7.077 r_long_range_B_refined 7.023 r_long_range_B_other 6.784 r_scangle_other 4.444 r_mcangle_other 4.155 r_mcangle_it 4.154 r_scbond_it 3.148 r_scbond_other 2.745 r_mcbond_it 2.65 r_mcbond_other 2.647 r_angle_refined_deg 1.709 r_angle_other_deg 0.802 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 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 1902 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing