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Crystal structure of nitrite reductase from Pseudoalteromonas haloplanktis TAC125
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KBW PDB ENTRY 1kbw, 1c52 experimental model PDB 1C52 PDB ENTRY 1kbw, 1c52
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 277 Lithium sulfate, Ammonium sulfate, Sodium citrate, Sucrose, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.338 α = 90 b = 180.338 β = 90 c = 180.338 γ = 90
Symmetry Space Group P 41 3 2
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 2007-09-29 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 1.95 43.8 99.1 72995 72995
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 1.95 2.02 99.3
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 1kbw, 1c52 1.95 8 63885 7167 99.21 0.16769 0.16564 0.1666 0.18604 0.1839 RANDOM 25.22
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.99 r_dihedral_angle_4_deg 18.419 r_dihedral_angle_3_deg 15.454 r_dihedral_angle_1_deg 6.96 r_scangle_it 3.643 r_scbond_it 2.334 r_angle_refined_deg 1.519 r_mcangle_it 1.365 r_mcbond_it 0.993 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.99 r_dihedral_angle_4_deg 18.419 r_dihedral_angle_3_deg 15.454 r_dihedral_angle_1_deg 6.96 r_scangle_it 3.643 r_scbond_it 2.334 r_angle_refined_deg 1.519 r_mcangle_it 1.365 r_mcbond_it 0.993 r_nbtor_refined 0.309 r_nbd_refined 0.222 r_symmetry_hbond_refined 0.201 r_symmetry_vdw_refined 0.191 r_chiral_restr 0.127 r_xyhbond_nbd_refined 0.12 r_metal_ion_refined 0.065 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3326 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling