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X-ray structure of the adduct formed upon reaction of ribonuclease A with the compound fac-[RuII(CO)3Cl2(N3-MBI), MBI=methyl-benzimidazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JVT 1JVT mol A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 22% PEG4K, 10 mM sodium citrate pH 5.1
Soaking: 3 days
Ligand con-centration: 5 mM
Crystal Properties Matthews coefficient Solvent content 2.21 44.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.651 α = 90 b = 32.983 β = 90.21 c = 73.046 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 2014-10-06 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 1.82 73.05 97.6 0.072 6.3 2.4 21285
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 1.82 1.85 95.4 0.384 1.7 1.4
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 mol A 1.82 73.05 20184 1091 95.14 0.16896 0.16546 0.1743 0.23577 0.2395 RANDOM 30.82
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] -0.48 -0.52 -0.11 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.322 r_dihedral_angle_3_deg 14.687 r_dihedral_angle_4_deg 14.169 r_long_range_B_refined 8.766 r_long_range_B_other 8.451 r_dihedral_angle_1_deg 7.266 r_mcangle_it 4.214 r_mcangle_other 4.213 r_scangle_other 4.098 r_scbond_it 2.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.322 r_dihedral_angle_3_deg 14.687 r_dihedral_angle_4_deg 14.169 r_long_range_B_refined 8.766 r_long_range_B_other 8.451 r_dihedral_angle_1_deg 7.266 r_mcangle_it 4.214 r_mcangle_other 4.213 r_scangle_other 4.098 r_scbond_it 2.848 r_mcbond_it 2.771 r_mcbond_other 2.766 r_scbond_other 2.661 r_angle_refined_deg 1.771 r_angle_other_deg 1.016 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 416 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing