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Crystal structure of Zea mays 3-phosphoglycerate dehydrogenase S282L mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 0.2M Sodium formate
0.2M Ammonium acetate
0.2M Sodium citrate tribasic dihydrate
0.2M Potassium sodium tartrate tetrahydrate
0.2M Sodium oxamate
1.0M Tris (base); BICINE pH8.5
40% v/v Ethylene glycol
20 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 4.26 71.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.345 α = 90 b = 96.345 β = 90 c = 503.003 γ = 120
Symmetry Space Group P 65 2 2
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 EIGER2 S 9M 2024-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97918 SSRF BL10U2
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 3.48 83.83 96.6 0.996 9.4 22.13 18472
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 3.48 7.77 1
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 3.48 22.97 1.34 18171 609 96.14 0.2119 0.2078 0.1944 0.2281 0.219
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 7.653 f_angle_d 1.462 f_chiral_restr 0.076 f_bond_d 0.013 f_plane_restr 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4432 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DIALS data reduction DIALS data scaling PHENIX phasing PHENIX refinement