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X-ray structure of the adduct formed upon reaction of lysozyme with the compound fac-[RuII(CO)3Cl2(N3-MIM), MIM=methyl-imidazole (crystals grown using NaCl)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 193L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 1.1M NaCl, 0.1 M sodium acetate pH 4.0
Crystal Properties Matthews coefficient Solvent content 1.97 37.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.573 α = 90 b = 78.573 β = 90 c = 36.664 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 RIGAKU SATURN 944 mirrors 2014-04-07 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 1.85 55.56 92.3 0.048 36.8 4.9 9488
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 1.85 1.88 0.603 2.3
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 193L 1.85 55.56 8981 457 92.08 0.163 0.15955 0.1686 0.2298 0.2336 RANDOM 33.256
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 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.271 r_dihedral_angle_4_deg 20.179 r_dihedral_angle_3_deg 14.362 r_dihedral_angle_1_deg 7.06 r_long_range_B_other 6.776 r_long_range_B_refined 6.774 r_scangle_other 5.073 r_scbond_it 3.573 r_mcangle_it 3.537 r_mcangle_other 3.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.271 r_dihedral_angle_4_deg 20.179 r_dihedral_angle_3_deg 14.362 r_dihedral_angle_1_deg 7.06 r_long_range_B_other 6.776 r_long_range_B_refined 6.774 r_scangle_other 5.073 r_scbond_it 3.573 r_mcangle_it 3.537 r_mcangle_other 3.535 r_scbond_other 3.445 r_mcbond_it 2.812 r_mcbond_other 2.765 r_angle_refined_deg 1.838 r_angle_other_deg 1.107 r_chiral_restr 0.123 r_bond_refined_d 0.027 r_gen_planes_refined 0.009 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 1000 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing