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Nitric oxide complex of the L16V mutant of cytochrome c prime from Alcaligenes xylosoxidans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 2.2M Ammonium sulfate
0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.74 55.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.199 α = 90 b = 53.199 β = 90 c = 180.679 γ = 120
Symmetry Space Group P 65 2 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 PIXEL DECTRIS PILATUS 6M-F 2012-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 SLS X10SA
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 1.38 46.072 100 0.051 15.4 7.6 32339
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 1.38 1.45 100 0.744 1 6.8
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 2YLI 1.38 46.07 30600 1633 99.98 0.1637 0.1626 0.1696 0.1858 0.1969 RANDOM 24.331
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] -0.21 -0.1 -0.21 0.67
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.824 r_dihedral_angle_2_deg 34.924 r_dihedral_angle_4_deg 22.861 r_dihedral_angle_3_deg 15.546 r_sphericity_bonded 13.661 r_dihedral_angle_1_deg 5.105 r_rigid_bond_restr 3.659 r_mcangle_it 3.485 r_mcbond_it 2.805 r_mcbond_other 2.725
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.824 r_dihedral_angle_2_deg 34.924 r_dihedral_angle_4_deg 22.861 r_dihedral_angle_3_deg 15.546 r_sphericity_bonded 13.661 r_dihedral_angle_1_deg 5.105 r_rigid_bond_restr 3.659 r_mcangle_it 3.485 r_mcbond_it 2.805 r_mcbond_other 2.725 r_angle_refined_deg 2.366 r_angle_other_deg 1.851 r_chiral_restr 0.116 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_gen_planes_other 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 948 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 70
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing