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Sulfite dehydrogenase from Starkeya Novella
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SOX PDB ENTRY 1SOX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 0.1M HEPES PH 7.4, 2.2M AMMONIUM SULFATE, 2% PEG200
Crystal Properties Matthews coefficient Solvent content 2.6 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.466 α = 90 b = 92.513 β = 90 c = 55.897 γ = 90
Symmetry Space Group P 21 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 CCD 2002-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2
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 1.8 17 95.6 0.06 9.1 5.7 259001
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 1.8 1.9 77.5 0.19 3.5 3
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 1SOX 1.8 20 43048 2295 95.3 0.138 0.136 0.1497 0.169 0.1794 RANDOM 11.84
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] 0.07 -0.25 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.708 r_dihedral_angle_4_deg 14.481 r_dihedral_angle_3_deg 12.355 r_dihedral_angle_1_deg 6.104 r_scangle_it 5.594 r_scbond_it 4.243 r_mcangle_it 2.886 r_mcbond_it 2.443 r_angle_refined_deg 1.34 r_angle_other_deg 0.775
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.708 r_dihedral_angle_4_deg 14.481 r_dihedral_angle_3_deg 12.355 r_dihedral_angle_1_deg 6.104 r_scangle_it 5.594 r_scbond_it 4.243 r_mcangle_it 2.886 r_mcbond_it 2.443 r_angle_refined_deg 1.34 r_angle_other_deg 0.775 r_symmetry_hbond_refined 0.298 r_nbd_refined 0.231 r_symmetry_vdw_other 0.198 r_nbd_other 0.189 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.16 r_symmetry_vdw_refined 0.116 r_nbtor_other 0.083 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3455 Nucleic Acid Atoms Solvent Atoms 584 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling CCP4 phasing