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Nitric oxide complex of the L16A mutant of cytochrome c prime from Alcaligenes xylosoxidans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YL0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 2.2 M Ammonium sulfate, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.76 55.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.629 α = 90 b = 53.629 β = 90 c = 180.523 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 2015-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.55 46.44 98.8 0.073 0.999 11.9 6.3 23047
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 1.55 1.63 98.1 0.76 1.9 6.5
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 2yl0 1.55 46.44 21801 1155 98.37 0.1728 0.1705 0.1849 0.2138 0.2216 RANDOM 22.068
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] -0.37 -0.19 -0.37 1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.506 r_sphericity_free 27.816 r_dihedral_angle_4_deg 19.954 r_sphericity_bonded 14.301 r_dihedral_angle_3_deg 13.954 r_dihedral_angle_1_deg 4.992 r_mcangle_it 2.852 r_mcbond_it 2.274 r_mcbond_other 2.252 r_rigid_bond_restr 2.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.506 r_sphericity_free 27.816 r_dihedral_angle_4_deg 19.954 r_sphericity_bonded 14.301 r_dihedral_angle_3_deg 13.954 r_dihedral_angle_1_deg 4.992 r_mcangle_it 2.852 r_mcbond_it 2.274 r_mcbond_other 2.252 r_rigid_bond_restr 2.251 r_angle_refined_deg 2.184 r_angle_other_deg 1.024 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 955 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SCALA data scaling PHASER phasing XDS data reduction