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Structure of putative oxidoreductase yvaA from Bacillus subtilis in triclinic form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GDO PDB entry 3GDO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1M Bis-tris pH 6.5, 25% PEG 3350, 0.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.52 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.931 α = 95.31 b = 92.135 β = 94.19 c = 187.589 γ = 95.21
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 2008-11-05 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.59 50 98.3 0.084 0.074 11.381 2.6 146417 146417
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.69 97.9 0.349 0.307 2.77 2.6 14589
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 PDB entry 3GDO 2.59 45.41 146360 7368 97.7 0.185 0.182 0.1845 0.236 0.2369 RANDOM 22.11
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] -0.25 -0.04 -0.87 0.31 -1.04 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.146 r_dihedral_angle_4_deg 18.475 r_dihedral_angle_3_deg 17.1 r_dihedral_angle_1_deg 6.019 r_scangle_it 3.072 r_scbond_it 1.782 r_angle_refined_deg 1.335 r_mcangle_it 1.121 r_mcbond_it 0.568 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.146 r_dihedral_angle_4_deg 18.475 r_dihedral_angle_3_deg 17.1 r_dihedral_angle_1_deg 6.019 r_scangle_it 3.072 r_scbond_it 1.782 r_angle_refined_deg 1.335 r_mcangle_it 1.121 r_mcbond_it 0.568 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31843 Nucleic Acid Atoms Solvent Atoms 516 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction MOLREP phasing