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Iron- and Nitric Oxide-bound structure of the engineered cyt b562 variant, CH3Y*
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M6T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 Drop consists of 2 uL of 25% PEP 426, 50 mM Magnesium Chloride and 0.1 M Bis-Tris (pH 6.0) mixed with 1 uL of 4 mM protein and 2.2 mM Iron(II) Sulfate (Anaerobic crystal growth). Diethylamine NONOate (5 mM) was added to mother liquor prior to crystal harvest
Crystal Properties Matthews coefficient Solvent content 2.26 45.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.919 α = 90 b = 98.69 β = 90 c = 178.99 γ = 90
Symmetry Space Group C 2 2 21
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 2018-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.73 ALS 5.0.2
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 1.955 49.345 99.5 0.089 0.998 28.5 12.6 31848
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.955 2.0039 98.1 0.192 0.992 12.2 12
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1m6t 1.955 49.345 1.4 31262 2000 98.11 0.206 0.203 0.2048 0.2486 0.2506
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 f_dihedral_angle_d 6.888 f_angle_d 0.405 f_chiral_restr 0.032 f_bond_d 0.019 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3311 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing