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Crystal structure of Arabidopsis thaliana cytosolic triosephosphate isomerase C13D mutant
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 0.2 M Sodium acetate trihydrate
0.1M TRIS hydrochloride 8.5
30% w/v Polyethylene glycol 4,000
Crystal Properties Matthews coefficient Solvent content 2.83 56.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.682 α = 90 b = 163.85 β = 90 c = 98.093 γ = 90
Symmetry Space Group C 2 2 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 CCD MARMOSAIC 300 mm CCD 2017-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 APS 21-ID-G
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 1.3 42.08 99.1 0.069 0.076 0.032 0.996 12 5.5 76329
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 1.3 1.32 97.8 0.435 0.48 0.2 0.921 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 1.3 41 72474 3839 98.95 0.1318 0.1306 0.13 0.1538 0.1535 RANDOM 14.438
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] 0.62 -1.06 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.988 r_sphericity_free 24.284 r_dihedral_angle_4_deg 12.318 r_sphericity_bonded 10.561 r_dihedral_angle_3_deg 9.933 r_dihedral_angle_1_deg 6.21 r_rigid_bond_restr 1.893 r_angle_refined_deg 1.591 r_angle_other_deg 1.591 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.988 r_sphericity_free 24.284 r_dihedral_angle_4_deg 12.318 r_sphericity_bonded 10.561 r_dihedral_angle_3_deg 9.933 r_dihedral_angle_1_deg 6.21 r_rigid_bond_restr 1.893 r_angle_refined_deg 1.591 r_angle_other_deg 1.591 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1846 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 7
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction