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Xanthomonas citri Dephospho-PGM in complex with xylose-1-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BMN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 22% PEG 8000, 0.2M MgCl, 0.1M HEPES
Crystal Properties Matthews coefficient Solvent content 2.02 39.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.863 α = 90 b = 54.626 β = 90 c = 173.359 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 CMOS RDI CMOS_8M 2016-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.00003 ALS 4.2.2
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 1.45 57.79 72.8 0.061 0.067 0.026 0.999 18.2 5.9 54627
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 1.45 1.47 70.5 0.642 0.762 0.398 0.564 1.6 3.3
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 5BMN 1.45 39.697 1.19 101364 5281 71.02 0.1792 0.1773 0.1776 0.2147 0.2139
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 4.444 f_angle_d 0.856 f_chiral_restr 0.077 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3432 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing