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Structural Genomics, the crystal structure of SpoVG from Bacillus subtilis subsp. subtilis str. 168
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I9X PDB ENTRY 2I9X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 277 0.2M Ammonium sulfate, 0.1M Sodium citrate, 15%(w/v)PEG4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.79 67.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.464 α = 90 b = 136.464 β = 90 c = 110.493 γ = 90
Symmetry Space Group P 41 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 ADSC QUANTUM 315 mirror 2006-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97711 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 3 47.95 99.9 0.135 13.6 5.5 21472 21472
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) 3 3.07 100 0.506 3.48 5.7 1406
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 (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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2I9X 3 47.95 20309 20309 1095 99.78 0.23014 0.23014 0.22671 0.2233 0.296 0.2909 RANDOM 38.683
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.018 r_dihedral_angle_3_deg 23.52 r_dihedral_angle_4_deg 19.088 r_dihedral_angle_1_deg 7.638 r_scangle_it 2.995 r_scbond_it 1.765 r_angle_refined_deg 1.602 r_mcangle_it 1.502 r_mcbond_it 0.829 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.018 r_dihedral_angle_3_deg 23.52 r_dihedral_angle_4_deg 19.088 r_dihedral_angle_1_deg 7.638 r_scangle_it 2.995 r_scbond_it 1.765 r_angle_refined_deg 1.602 r_mcangle_it 1.502 r_mcbond_it 0.829 r_nbtor_refined 0.317 r_symmetry_hbond_refined 0.297 r_nbd_refined 0.255 r_symmetry_vdw_refined 0.248 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.11 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4351 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing