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Crystal structure of oxidoreductase, Gfo/Idh/MocA family from Streptococcus pneumoniae with reductive methylated Lysine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 0.2 M Lithium sulfate, 0.1 M TRIS, 1.26 M Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.31 46.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.915 α = 90 b = 152.386 β = 103.12 c = 100.237 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315r 2012-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97940 APS 19-ID
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 50 99.7 0.074 25.3 3.7 91010 90011 -3
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 2.07 98.6 0.17 7 3.3 8840
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2 38.6 89975 89975 4514 99.56 0.1481 0.1481 0.1455 0.1547 0.1952 0.2017 RANDOM 17.5895
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] 0.41 0.15 -0.37 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.141 r_sphericity_free 29.672 r_dihedral_angle_4_deg 15.46 r_dihedral_angle_3_deg 12.528 r_sphericity_bonded 6.474 r_dihedral_angle_1_deg 5.903 r_rigid_bond_restr 2.677 r_angle_refined_deg 1.111 r_angle_other_deg 0.718 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.141 r_sphericity_free 29.672 r_dihedral_angle_4_deg 15.46 r_dihedral_angle_3_deg 12.528 r_sphericity_bonded 6.474 r_dihedral_angle_1_deg 5.903 r_rigid_bond_restr 2.677 r_angle_refined_deg 1.111 r_angle_other_deg 0.718 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9753 Nucleic Acid Atoms Solvent Atoms 904 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing MLPHARE phasing DM phasing SHELXDE phasing ARP/wARP model building RESOLVE phasing Coot model building