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Nitric oxide complex of the L16F 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
0.1M Hepes pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.76 55.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.207 α = 90 b = 53.207 β = 90 c = 181.39 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 2015-10-10 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) Rrim I (All) Rpim I (All) 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 1.7 46.08 100 0.059 0.065 0.026 0.998 12.7 6.2 17754
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 1.7 1.73 100 0.832 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 2YLI 1.7 46.08 16830 829 99.89 0.214 0.2119 0.2195 0.258 0.2699 RANDOM 34.44
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] 0.04 0.02 0.04 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.168 r_dihedral_angle_4_deg 19.86 r_dihedral_angle_3_deg 14.398 r_dihedral_angle_1_deg 5.575 r_angle_other_deg 3.687 r_angle_refined_deg 2.341 r_mcangle_it 1.658 r_mcbond_it 1.146 r_mcbond_other 1.146 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.168 r_dihedral_angle_4_deg 19.86 r_dihedral_angle_3_deg 14.398 r_dihedral_angle_1_deg 5.575 r_angle_other_deg 3.687 r_angle_refined_deg 2.341 r_mcangle_it 1.658 r_mcbond_it 1.146 r_mcbond_other 1.146 r_chiral_restr 0.104 r_bond_refined_d 0.017 r_gen_planes_other 0.017 r_gen_planes_refined 0.01 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 943 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 59
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data scaling PHASER phasing XDS data reduction