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Xanthomonas citri Phospho-PGM in complex with glucose-1,6-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 7.5 277 22% PEG 8000, 0.2M MgCl, 0.1M HEPES
Crystal Properties Matthews coefficient Solvent content 2.02 39.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.69 α = 90 b = 54.72 β = 90 c = 173.69 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 2018-03-28 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 1.46 46.3 100 0.145 0.151 0.041 0.999 14.4 13.3 73467
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 1.46 1.48 100 2.15 2.286 0.759 0.345 0.8 8.8
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 1.46 46.296 0.05 73378 3666 99.98 0.1711 0.1691 0.1701 0.2071 0.2076
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 6.611 f_angle_d 0.848 f_chiral_restr 0.08 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3450 Nucleic Acid Atoms Solvent Atoms 755 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing