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High Resolution Crystal Structure of the Escherichia coli Cytochrome c Nitrite Reductase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GU6 PDB ENTRY 1GU6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 Crystals were obtained in 100 mM HEPES pH 7.5, 20 % PEG 10 K. , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.44 49.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.46 α = 90 b = 79.3 β = 101.57 c = 137.58 γ = 90
Symmetry Space Group P 1 21 1
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 MAR CCD 165 mm 2004-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 1.74 134.84 99.1 0.073 0.073 7.7 3.9 193642 193642 16.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.83 94.1 0.351 0.351 2.1 3.1 26673
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 1GU6 1.74 39.65 2.8 193618 193618 9756 99.14 0.156 0.156 0.154 0.1538 0.189 0.1882 RANDOM 16.781
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] -0.01 -0.01 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.435 r_dihedral_angle_4_deg 15.196 r_dihedral_angle_3_deg 13.472 r_dihedral_angle_1_deg 5.571 r_scangle_it 2.838 r_scbond_it 1.875 r_angle_refined_deg 1.298 r_mcangle_it 1.098 r_mcbond_it 0.691 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.435 r_dihedral_angle_4_deg 15.196 r_dihedral_angle_3_deg 13.472 r_dihedral_angle_1_deg 5.571 r_scangle_it 2.838 r_scbond_it 1.875 r_angle_refined_deg 1.298 r_mcangle_it 1.098 r_mcbond_it 0.691 r_nbtor_refined 0.295 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.198 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.088 r_metal_ion_refined 0.069 r_bond_refined_d 0.013 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13904 Nucleic Acid Atoms Solvent Atoms 2149 Heterogen Atoms 1000
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection