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Myoglobin variant Mb-imi complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M8F 6M8F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 296 Mb(H64G,V68A) at 3.6 mM in 20 mM Tris-HCl pH 8.4, 1 mM EDTA, was mixed with an equal volume of reservoir solution (200 mM Tris-HCl pH 8.9 and 2.46 M ammonium sulfate). The crystal was dunked in a cryoprotection solution (reservoir buffer supplemented with 9% sucrose (w/v), 2% glucose (w/v), 8% glycerol (v/v), and 8% ethylene glycol (v/v)) prior to being flash-frozen in liquid nitrogen. Note that imidazole was present in lysis buffer at 10 mM prior to two-step purification.
Crystal Properties Matthews coefficient Solvent content 3.11 60.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.425 α = 90 b = 90.425 β = 90 c = 45.442 γ = 120
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 2019-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
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 1.04 78.31 99.6 0.067 0.022 0.995 18.2 9.2 101447 8.65
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.04 1.06 0.504 0.234 0.817 2.7
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 6M8F 1.04 78.31 1.35 101444 5080 99.6 0.129 0.1284 0.1282 0.1406 0.1402 15.27
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 14.4027 f_angle_d 1.0192 f_chiral_restr 0.0781 f_bond_d 0.0076 f_plane_restr 0.0064
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1207 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing