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Reduced and cyanide-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O0R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 277 100mM sodium citrate, pH 6.0, vapor diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.08 69.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.688 α = 90 b = 107.381 β = 90 c = 195.288 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 RAYONIX MX225HE mirrors 2012-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00 SPring-8 BL41XU
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 2.49 50 99.1 0.076 0.076 24.231 7.4 66399 -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 2.5 2.59 100 0.526 0.526 3.684 7.5
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 3O0R 2.49 35.16 66111 3358 98.39 0.1907 0.1888 0.1937 0.2274 0.2288 RANDOM 61.6746
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] -0.83 -0.7 1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.476 r_dihedral_angle_4_deg 21.612 r_dihedral_angle_3_deg 20.202 r_dihedral_angle_1_deg 6.646 r_angle_refined_deg 1.808 r_angle_other_deg 0.98 r_chiral_restr 0.112 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.476 r_dihedral_angle_4_deg 21.612 r_dihedral_angle_3_deg 20.202 r_dihedral_angle_1_deg 6.646 r_angle_refined_deg 1.808 r_angle_other_deg 0.98 r_chiral_restr 0.112 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8060 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 201
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SPACE data collection HKL-2000 data reduction HKL-2000 data scaling