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Structure of the Shewanella loihica PV-4 NADH-dependent persulfide reductase C531S Mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ICR PDB ENTRY 3ICR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.7 298 50 mM Na acetate, 200 mM ammonium acetate, 5% PEG 8K, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.36 63.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.737 α = 90 b = 133.737 β = 90 c = 79.713 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2009-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.99 116 99.3 0.092 15.8 4.5 103268 103268 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.07 99.7 0.41 6.9
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 PDB ENTRY 3ICR 1.99 115.85 108806 103268 5538 99.32 0.15958 0.15824 0.2386 0.18465 0.275 RANDOM 33.884
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] -22.26 -22.26 44.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.331 r_dihedral_angle_4_deg 20.574 r_dihedral_angle_3_deg 17.636 r_dihedral_angle_1_deg 7.486 r_scangle_it 5.531 r_scbond_it 3.909 r_angle_refined_deg 2.353 r_mcangle_it 2.202 r_mcbond_it 1.434 r_chiral_restr 0.186
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.331 r_dihedral_angle_4_deg 20.574 r_dihedral_angle_3_deg 17.636 r_dihedral_angle_1_deg 7.486 r_scangle_it 5.531 r_scbond_it 3.909 r_angle_refined_deg 2.353 r_mcangle_it 2.202 r_mcbond_it 1.434 r_chiral_restr 0.186 r_bond_refined_d 0.029 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 8589 Nucleic Acid Atoms Solvent Atoms 607 Heterogen Atoms 204
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection PHASER phasing