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A Circular Permutant of the Tobacco Mosaic Virus (TMV) mutant Q101H coordinated with heme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KML
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 The apoprotein crystals were obtained in 0.1 M SPG buffer (0.0125 M succinic acid, 0.0438 M sodium phosphate, 0.0437 M glycine), 12-18 % (v/v) PEG 1500, pH 5.0-5.5. The holoprotein crystals were obtained by transferring the apoprotein crystals into a soak-in buffer at the same pH as their mother liquor containing 0.1 M SPG buffer, 30%-40% (v/v) PEG 1500, 150-300 uM hemin (iron (III) protoporphyrin IX)
Crystal Properties Matthews coefficient Solvent content 3.1 60.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 218.015 α = 90 b = 176.136 β = 98.53 c = 100.235 γ = 90
Symmetry Space Group C 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 PILATUS3 S 6M 2017-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1158 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3 136.4 100 0.983 4.5 12.3 74780 59.01
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.06 100 0.317 12.3
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 3KML 3 49.56 1.33 74385 2039 99.49 0.257 0.2568 0.2547 0.2651 0.262 Imported from pdb 3KML 58.77
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 9.0576 f_angle_d 0.5014 f_chiral_restr 0.0361 f_plane_restr 0.0028 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18598 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 387
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling