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Crystal structure of nitrite reductase from Hyphomicrobium denitrificans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KBW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 PEG4000, potassium thiocyanate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.4 63.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.551 α = 90 b = 162.551 β = 90 c = 148.97 γ = 90
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 2005-05-19 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 2.2 48.59 99.7 195178 195178
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.28 100
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1kbw 2.2 8 194626 180940 9588 99.77 0.15233 0.15164 0.1653 0.1489 RANDOM 28.525
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] -0.1 -0.1 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.769 r_dihedral_angle_4_deg 25.264 r_dihedral_angle_3_deg 18.119 r_dihedral_angle_1_deg 7.552 r_scangle_it 3.93 r_scbond_it 2.441 r_angle_refined_deg 1.839 r_mcangle_it 1.574 r_mcbond_it 0.848 r_metal_ion_refined 0.367
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.769 r_dihedral_angle_4_deg 25.264 r_dihedral_angle_3_deg 18.119 r_dihedral_angle_1_deg 7.552 r_scangle_it 3.93 r_scbond_it 2.441 r_angle_refined_deg 1.839 r_mcangle_it 1.574 r_mcbond_it 0.848 r_metal_ion_refined 0.367 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.223 r_symmetry_hbond_refined 0.207 r_chiral_restr 0.172 r_xyhbond_nbd_refined 0.142 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19260 Nucleic Acid Atoms Solvent Atoms 1803 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing