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Crystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant AIFQ (Y7A/M38I/Y83F/C106Q)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VJ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 8 mg/ml protein concentration
0.1 M Tris pH 8.5
2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 1.95 36.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.795 α = 90 b = 53.733 β = 90 c = 90.435 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 2M 2017-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.000 ELETTRA 5.2R
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 1.7 34.6 99.75 0.08215 0.03552 0.997 12.75 6.4 23041 23.91
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 1.7 1.761 0.653 0.2754 0.836 2.82
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 1vj2 1.7 34.6 1.35 23038 1155 99.77 0.2105 0.2088 0.2086 0.2416 0.2418 28.96
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 25.5198 f_angle_d 0.8025 f_chiral_restr 0.0598 f_plane_restr 0.0065 f_bond_d 0.0045
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1766 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHASER phasing