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Structure of the Shewanella loihica PV-4 NADH-dependent persulfide reductase
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 8000, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.35 63.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.343 α = 90 b = 134.343 β = 90 c = 81.235 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 Si 111 Channel 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 2.01 117 99.5 0.086 13.8 10.4 101779 101779 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 2.01 2.08 96.4 0.449 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 3ICR 2.01 116.37 2 101779 101779 5440 97.79 0.13923 0.13923 0.13734 0.1669 0.1731 0.189 RANDOM 37.84
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] -29.53 -29.53 59.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.122 r_dihedral_angle_4_deg 21.062 r_dihedral_angle_3_deg 17.707 r_dihedral_angle_1_deg 7.848 r_scangle_it 6.437 r_scbond_it 4.669 r_angle_refined_deg 2.73 r_mcangle_it 2.417 r_mcbond_it 1.553 r_chiral_restr 0.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.122 r_dihedral_angle_4_deg 21.062 r_dihedral_angle_3_deg 17.707 r_dihedral_angle_1_deg 7.848 r_scangle_it 6.437 r_scbond_it 4.669 r_angle_refined_deg 2.73 r_mcangle_it 2.417 r_mcbond_it 1.553 r_chiral_restr 0.225 r_bond_refined_d 0.038 r_gen_planes_refined 0.014 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 545 Heterogen Atoms 204
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling