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Crystal Structure of BAY 60-2770 bound C139A H-NOX domain with S-nitrosylated conserved C122
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O0C PDB ENTRY 2O0C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 1.8M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.76 67.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.573 α = 90 b = 122.573 β = 90 c = 122.573 γ = 90
Symmetry Space Group P 21 3
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 RIGAKU SATURN 944+ mirrors 2011-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 86.7 99.25 0.069 20.7 6.9 14582 14472 1 1 29.7
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 2.8 2.93 99.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 2O0C 2.8 86.69 2.3 14582 14472 807 99.25 0.1657 0.165 0.1628 0.1699 0.21763 0.218 RANDOM 29.702
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 22.68 r_dihedral_angle_4_deg 11.844 r_dihedral_angle_3_deg 10.399 r_dihedral_angle_1_deg 2.122 r_angle_refined_deg 0.889 r_angle_other_deg 0.601 r_scangle_it 0.512 r_mcangle_it 0.324 r_scbond_it 0.286 r_mcbond_it 0.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.68 r_dihedral_angle_4_deg 11.844 r_dihedral_angle_3_deg 10.399 r_dihedral_angle_1_deg 2.122 r_angle_refined_deg 0.889 r_angle_other_deg 0.601 r_scangle_it 0.512 r_mcangle_it 0.324 r_scbond_it 0.286 r_mcbond_it 0.173 r_chiral_restr 0.062 r_mcbond_other 0.014 r_gen_planes_refined 0.011 r_bond_refined_d 0.003 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2866 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 104
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling