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Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 in complex with L-malate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 30%PEG400, 0.1 M Hepes Sodium Salt pH 7.5, 200mM Magnesium Chloride
Crystal Properties Matthews coefficient Solvent content 4.1 70.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.08 α = 90 b = 352.2 β = 101.84 c = 176.04 γ = 90
Symmetry Space Group P 1 21 1
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 X 16M 2019-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.981 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.142 50 99.3 0.292 0.993 6.94 7.11 237667 82.2502477245
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.143 3.33 96.1 2.102 0.352 0.89 6.42
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 3.14239899937 48.9254741206 1.3280661634 237518 11875 99.3022196022 0.20393187438 0.202062209888 0.2124 0.239756715239 0.2476 75.9200195511
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 12.6769235459 f_angle_d 0.836808905316 f_chiral_restr 0.0470090510351 f_plane_restr 0.00598719539062 f_bond_d 0.00577833186256
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 58490 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 295
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing