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Crystal structure of an oxidoreductase from Sinorhizobium meliloti 1021
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D3W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2M MgCl2, 0.1M HEPES pH 7.5, 30% (v/v) PEG550MME, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.225 α = 90 b = 84.225 β = 90 c = 249.238 γ = 120
Symmetry Space Group P 32 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 PIXEL PSI PILATUS 6M mirrors 2011-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
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 2.45 50 100 0.08 6 21.2 38775 38775
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 2.45 2.54 100 0.7 4 21.2 3804
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3D3W 2.45 47.38 38775 36644 1939 99.69 0.18764 0.18486 0.1816 0.24062 0.2367 RANDOM 34.217
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 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.442 r_dihedral_angle_4_deg 22.435 r_dihedral_angle_3_deg 18.378 r_dihedral_angle_1_deg 6.792 r_scangle_it 5.522 r_scbond_it 3.338 r_mcangle_it 1.923 r_angle_refined_deg 1.881 r_mcbond_it 0.997 r_chiral_restr 0.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.442 r_dihedral_angle_4_deg 22.435 r_dihedral_angle_3_deg 18.378 r_dihedral_angle_1_deg 6.792 r_scangle_it 5.522 r_scbond_it 3.338 r_mcangle_it 1.923 r_angle_refined_deg 1.881 r_mcbond_it 0.997 r_chiral_restr 0.128 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7034 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement