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Crystal structure of Bradyrhizobium japonicum ScoI in the oxidized state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TXO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 0.1M SPG, 25% PEG15000
Crystal Properties Matthews coefficient Solvent content 2.1 41.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.776 α = 90 b = 82.629 β = 90.03 c = 45.853 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 80 PIXEL DECTRIS PILATUS 6M 2014-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.3 45.8 91.9 0.039 0.042 28.35 7 65098 -3 15.447
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.33 83.6 0.151 0.163 9.94
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 4txo 1.3 45.8 65098 3255 91.86 0.106 0.1041 0.1039 0.1418 0.1416 RANDOM 13.3
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] -0.13 -0.13 0.15 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.958 r_sphericity_free 31.522 r_dihedral_angle_4_deg 20.737 r_dihedral_angle_3_deg 12.06 r_sphericity_bonded 12.039 r_dihedral_angle_1_deg 6.352 r_rigid_bond_restr 5.687 r_mcangle_it 2.508 r_angle_refined_deg 2.051 r_mcbond_it 1.913
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.958 r_sphericity_free 31.522 r_dihedral_angle_4_deg 20.737 r_dihedral_angle_3_deg 12.06 r_sphericity_bonded 12.039 r_dihedral_angle_1_deg 6.352 r_rigid_bond_restr 5.687 r_mcangle_it 2.508 r_angle_refined_deg 2.051 r_mcbond_it 1.913 r_mcbond_other 1.913 r_angle_other_deg 1.023 r_chiral_restr 0.128 r_bond_refined_d 0.022 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 2455 Nucleic Acid Atoms Solvent Atoms 490 Heterogen Atoms 16
Software Software Software Name Purpose XDS data reduction REFMAC refinement PDB_EXTRACT data extraction XSCALE data scaling PHASER phasing XSCALE data reduction