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Crystal structure of Thermoglobin Y29F mutant in complex with imidazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VHB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 3.0 M ammonium sulfide, 0.1 M sodium cacodylate pH 6.0, 2 % PEG 400
Crystal Properties Matthews coefficient Solvent content 2.26 45.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.771 α = 90 b = 35.823 β = 95.2 c = 138.084 γ = 90
Symmetry Space Group I 1 2 1
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 EIGER X 16M 2020-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.5 38.03 99.5 0.039 0.046 0.024 18.8 6.6 46830
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 93.1 0.626 0.807 0.501 1.8 4.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1vhb 1.5 38.022 1.33 46816 4417 99.36 0.2004 0.1993 0.1999 0.2232 0.2258 Random selection
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 17.071 f_angle_d 0.829 f_chiral_restr 0.042 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2177 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 101
Software Software Software Name Purpose PHENIX refinement XDS data processing BUCCANEER model building MOLREP phasing XDS data reduction Aimless data scaling