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Crystal structure of oxy-I107E CuB myoglobin (I107E L29H F43H sperm whale myoglobin; partial occupancy)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FWX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.6 277 1.5-2.0 mM protein in 20 mM tris sulfate pH 8.0 buffer, mixed 1:1 with crystallization solution composed of 100 mM tris sulfate pH 8.6, 200 mM sodium acetate, and 30% w/v PEG 10000. After crystalization, soaked, under anaerobic conditions, in 20 mM dithionite for 10 minutes, and washed with anaerobic buffer. Reduced crystals were sealed in an air-tight bomb and pressurized at ~1500 psi O2 for up to 10 minutes. Crystals were harvested and cryocooled after a brief soak in 50% PEG 400 supersaturated with O2.
Crystal Properties Matthews coefficient Solvent content 2.1 41.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.845 α = 90 b = 46.982 β = 90 c = 78.034 γ = 90
Symmetry Space Group P 21 21 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 2015-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.98 SSRL BL11-1
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 1.18 39.02 97 0.024 0.028 0.013 1 31.7 3.9 47352
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.18 1.2 63.4 0.216 0.275 0.169 0.902 2.1
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 4FWX 1.18 39.02 1.34 86347 4119 92.81 0.1582 0.1566 0.1604 0.1902 0.1921 17.26
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 14.941 f_angle_d 1.3967 f_chiral_restr 0.1015 f_bond_d 0.0127 f_plane_restr 0.0107
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1219 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHENIX phasing