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Crystal structure of electron transfer complex of nitrite reductase with cytochrome c
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OE1 PDB ENTRY 1oe1, 1kx7 experimental model PDB 1KX7 PDB ENTRY 1oe1, 1kx7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 277 PEG 3350, Magnesium acetate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.27 45.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.345 α = 90 b = 103.942 β = 90 c = 163.144 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 100 CCD Bruker DIP-6040 2007-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.7 43.8 98.8 119863 119863
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 1.7 1.76 97.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1oe1, 1kx7 1.7 8 105332 11727 98.78 0.16548 0.16217 0.1618 0.19542 0.1942 RANDOM 18.525
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] -0.74 1 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.604 r_dihedral_angle_4_deg 20.154 r_dihedral_angle_3_deg 13.887 r_dihedral_angle_1_deg 11.835 r_scangle_it 3.188 r_scbond_it 2.007 r_angle_refined_deg 1.496 r_mcangle_it 1.139 r_mcbond_it 0.762 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.604 r_dihedral_angle_4_deg 20.154 r_dihedral_angle_3_deg 13.887 r_dihedral_angle_1_deg 11.835 r_scangle_it 3.188 r_scbond_it 2.007 r_angle_refined_deg 1.496 r_mcangle_it 1.139 r_mcbond_it 0.762 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.201 r_chiral_restr 0.118 r_xyhbond_nbd_refined 0.116 r_symmetry_hbond_refined 0.112 r_metal_ion_refined 0.022 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8242 Nucleic Acid Atoms Solvent Atoms 1073 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling