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NADH oxidase /nitrite reductase from Pyrococcus furiosus Pfu-1140779-001
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F3P pdb entry 1F3P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 modified microbatch 3.8 315 14%w/v PEG-4000, 0.15M sodium chloride, 0.15M magnesium chloride, 0.1M sodium acetate, modified microbatch, temperature 315K, pH 3.8 2 modified microbatch 3.8 315 18%w/v PEG-4000, 0.15M sodium chloride, 0.15M magnesium chloride, 0.1M sodium acetate, modified microbatch, temperature 315K, pH 3.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.335 α = 90 b = 73.737 β = 90 c = 95.849 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 ADSC QUANTUM 210 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD ADSC QUANTUM 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-ID 2 SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.15 20 92.2 0.112 22114
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.15 2.32 64.5 0.474
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 (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 1F3P 2.35 58.722 18210 915 99.378 0.202 0.20202 0.2 0.2082 0.2412 0.2495 RANDOM 37.008
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] 0.689 0.965 -1.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.402 r_dihedral_angle_4_deg 20.027 r_dihedral_angle_3_deg 14.946 r_dihedral_angle_1_deg 6.553 r_scangle_it 2.457 r_scbond_it 1.558 r_angle_refined_deg 1.407 r_mcangle_it 1.062 r_scangle_other 0.921 r_angle_other_deg 0.793
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.402 r_dihedral_angle_4_deg 20.027 r_dihedral_angle_3_deg 14.946 r_dihedral_angle_1_deg 6.553 r_scangle_it 2.457 r_scbond_it 1.558 r_angle_refined_deg 1.407 r_mcangle_it 1.062 r_scangle_other 0.921 r_angle_other_deg 0.793 r_mcbond_it 0.77 r_scbond_other 0.589 r_mcangle_other 0.511 r_symmetry_vdw_refined 0.308 r_symmetry_vdw_other 0.205 r_nbd_refined 0.189 r_nbtor_refined 0.172 r_nbd_other 0.169 r_symmetry_hbond_refined 0.161 r_xyhbond_nbd_refined 0.136 r_mcbond_other 0.127 r_chiral_restr 0.084 r_nbtor_other 0.08 r_xyhbond_nbd_other 0.031 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2637 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 53
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CNS phasing