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The 1.06 A resolution structure of the L16G mutant of ferric cytochrome c prime from Alcaligenes xylosoxidans, complexed with nitrite
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YL7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 50 mM sodium nitrite, 2.2 M ammonium sulphate and 0.1 M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.86 56.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.91 α = 90 b = 53.91 β = 90 c = 183.21 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 2017-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.06 45.24 96.8 0.063 0.023 1 13.1 7.7 70168 8.53
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.06 1.08 99 0.493 0.587 5.1
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 2yl7 1.06 45.24 66609 3506 96.7 0.1787 0.17758 0.1728 0.20005 0.1921 RANDOM 14.673
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] 0.64 0.32 0.64 -2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.577 r_sphericity_free 24.608 r_dihedral_angle_4_deg 14.306 r_dihedral_angle_3_deg 11.838 r_sphericity_bonded 8.705 r_rigid_bond_restr 5.736 r_dihedral_angle_1_deg 5.513 r_long_range_B_refined 3.653 r_long_range_B_other 3.651 r_angle_refined_deg 2.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.577 r_sphericity_free 24.608 r_dihedral_angle_4_deg 14.306 r_dihedral_angle_3_deg 11.838 r_sphericity_bonded 8.705 r_rigid_bond_restr 5.736 r_dihedral_angle_1_deg 5.513 r_long_range_B_refined 3.653 r_long_range_B_other 3.651 r_angle_refined_deg 2.179 r_scangle_other 1.733 r_scbond_it 1.49 r_scbond_other 1.485 r_angle_other_deg 1.457 r_mcangle_it 1.384 r_mcangle_other 1.384 r_mcbond_it 1.05 r_mcbond_other 1.044 r_chiral_restr 0.083 r_gen_planes_refined 0.017 r_bond_refined_d 0.016 r_gen_planes_other 0.011 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 945 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing