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Laue structure of Shewanella oneidensis cytochrome-c Nitrite Reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RDZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.25 296 14% PEG 4K, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.79 55.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.5 α = 90 b = 95.9 β = 90 c = 223.8 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 273 CCD MAR CCD 165 mm 2011-06-17 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 1.05-1.15 APS 14-ID-B
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 2.59 100 100 0.099 0.099 16.7 7.7 25875 25875
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 2.59 2.72 40.5 7.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2RDZ 2.59 40.56 2 24561 24561 1315 100 0.195 0.195 0.19024 0.193 0.28462 0.2825 RANDOM 22.071
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] 0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.973 r_dihedral_angle_3_deg 21.008 r_dihedral_angle_4_deg 15.893 r_dihedral_angle_1_deg 8.062 r_scangle_it 1.784 r_angle_refined_deg 1.531 r_scbond_it 1.095 r_angle_other_deg 0.945 r_mcangle_it 0.862 r_mcbond_it 0.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.973 r_dihedral_angle_3_deg 21.008 r_dihedral_angle_4_deg 15.893 r_dihedral_angle_1_deg 8.062 r_scangle_it 1.784 r_angle_refined_deg 1.531 r_scbond_it 1.095 r_angle_other_deg 0.945 r_mcangle_it 0.862 r_mcbond_it 0.463 r_chiral_restr 0.081 r_mcbond_other 0.067 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6946 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 432
Software Software Software Name Purpose LaueCollect data collection PHASER phasing REFMAC refinement Precognition data reduction Epinorm data reduction