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Crystal structure of C14S mutant of triosephosphate isomerase from Chamydomonas reinhardtii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MKN wild-type protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.1 M Bis-Tris (pH 5.0) and 17.5% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 4.2 70.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.975 α = 90 b = 99.478 β = 90 c = 102.376 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 EIGER R 4M 2021-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9677 ESRF ID30B
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 3.55 98.97 99 0.445 0.485 0.19 0.972 4.3 6.4 12570 -3 3
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 3.55 3.89 1.565 1.715 0.686 0.521 1.5 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.55 21.65 0.03 12459 1240 98.88 0.28 0.279 0.2746 0.2985 0.2802 53.71
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 6.31 f_angle_d 0.582 f_chiral_restr 0.042 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3786 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement SCALA data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction