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Structure of the Shewanella loihica PV-4 NADH-dependent persulfide reductase C43S/C531S Double 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 4.7 298 200 mM ammonium acetate, 50 mM sodium citrate, 5% PEG 4000, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.24 62.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.705 α = 90 b = 133.705 β = 90 c = 79.238 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 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 115 101510 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 97.5
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 2 115 101510 101510 5143 99.5 0.124 0.122 0.1776 0.155 0.2074 RANDOM 35.703
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] -20.84 -20.84 41.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.83 r_dihedral_angle_4_deg 19.097 r_dihedral_angle_3_deg 17.682 r_dihedral_angle_1_deg 7.637 r_scangle_it 6.254 r_scbond_it 4.516 r_angle_refined_deg 2.622 r_mcangle_it 2.44 r_mcbond_it 1.505 r_chiral_restr 0.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.83 r_dihedral_angle_4_deg 19.097 r_dihedral_angle_3_deg 17.682 r_dihedral_angle_1_deg 7.637 r_scangle_it 6.254 r_scbond_it 4.516 r_angle_refined_deg 2.622 r_mcangle_it 2.44 r_mcbond_it 1.505 r_chiral_restr 0.211 r_bond_refined_d 0.031 r_gen_planes_refined 0.013 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 549 Heterogen Atoms 204
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling