Navigation Tabs XN joint refinement of manganese catalase from Thermus Thermophilus HB27
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V8U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 293 1.95 M Ammonium Sulfate d-8, 14.5v/v% ethylenglycol, 50 mM AMPSO buffer pD 9.6. Drop: 32 mg/mL of manganese catalase was mixed with equal volume of Reservoir.
Crystal Properties Matthews coefficient Solvent content 2.97 58.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.396 α = 90 b = 133.396 β = 90 c = 133.396 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS PILATUS 6M Focusing mirrors with rhodium coated silicon single crystal 2017-03-20 M SINGLE WAVELENGTH 2 1 neutron 293 Ni-Ti supermirror neutron guide Detector: iBIXDetector type: WSF PSD (Wavelength Shift Fiber Position Sensitive Detector) 2016-12-01 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A 2 SPALLATION SOURCE J-PARC MLF BEAMLINE BL-03 3-6 JPARC MLF BL-03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (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 1.37 44.5 100 0.092 0.03 25.7 9.8 164892 -3 16.08 2 2.349 14.4 98.2 0.322 0.151 4.5 5.2 32509 -3 16.08
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.37 1.39 0.956 0.365 1.8 8.4 2 2.35 2.43 0.742 0.381 1.4 4.4
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1.37 44.465 1.33 164816 8232 99.98 0.1228 0.1222 0.1332 Random selection NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.349 14.384 -2 32494 1622 98.23 0.1536 0.1516 0.191 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 18.388 f_dihedral_angle_d 18.388 f_angle_d 1.261 f_angle_d 1.261 f_chiral_restr 0.23 f_chiral_restr 0.23 f_bond_d 0.007 f_bond_d 0.007 f_plane_restr 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4572 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 23
Software Software Software Name Purpose PHENIX refinement Coot model building