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X-ray structure of free methionine-R-sulfoxide reductase from neisseria meningitidis in complex with its substrate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.25 293 23% MPD, 120 mM Mg(CH3COO)2, 100 mM cacodylate, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.01 38.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.32 α = 104.17 b = 39.48 β = 105.16 c = 52.25 γ = 100.5
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 ADSC QUANTUM 315r 2008-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.886 SOLEIL PROXIMA 1
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 1.2 25 84.4 0.039 19.91 8.54 75066 -3 18.941
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) 1.2 1.23 37.4 0.418 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.25 20 70912 3545 100 0.12 0.118 0.1288 0.157 0.1626 RANDOM 19.68
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] 0.3 0.09 0.08 -0.03 0.01 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.659 r_dihedral_angle_4_deg 17.203 r_dihedral_angle_3_deg 12.176 r_dihedral_angle_1_deg 7.406 r_scangle_it 6.8 r_scbond_it 5.065 r_mcangle_it 3.516 r_mcbond_it 2.488 r_angle_refined_deg 2.286 r_rigid_bond_restr 2.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.659 r_dihedral_angle_4_deg 17.203 r_dihedral_angle_3_deg 12.176 r_dihedral_angle_1_deg 7.406 r_scangle_it 6.8 r_scbond_it 5.065 r_mcangle_it 3.516 r_mcbond_it 2.488 r_angle_refined_deg 2.286 r_rigid_bond_restr 2.258 r_angle_other_deg 1.24 r_mcbond_other 0.865 r_chiral_restr 0.285 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2564 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 69
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction