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Structure of 3-phospho-D-glycerate guanylyltransferase with product 3-GPPG bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BWG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 10% PEG 3000, 200 mm MgCl2, 100 mm sodium cacodylate pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.56 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.09 α = 90 b = 57.09 β = 90 c = 228.97 γ = 120
Symmetry Space Group P 32 2 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 PILATUS 2M Si111 2021-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 2.35 50 99.9 0.465 0.489 0.975 5.4 10.1 18963 -3 29.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.49 99.4 1.805 1.898 0.511 1.3 10.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6bwg 2.35 49.49 18962 878 99.832 0.189 0.1865 0.1867 0.2381 0.2373 26.473
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] 0.004 0.002 0.004 -0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.429 r_dihedral_angle_4_deg 19.79 r_dihedral_angle_3_deg 15.585 r_dihedral_angle_1_deg 7.321 r_lrange_it 3.109 r_lrange_other 3.099 r_angle_refined_deg 1.822 r_scangle_it 1.731 r_scangle_other 1.73 r_angle_other_deg 1.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.429 r_dihedral_angle_4_deg 19.79 r_dihedral_angle_3_deg 15.585 r_dihedral_angle_1_deg 7.321 r_lrange_it 3.109 r_lrange_other 3.099 r_angle_refined_deg 1.822 r_scangle_it 1.731 r_scangle_other 1.73 r_angle_other_deg 1.299 r_mcangle_other 1.159 r_mcangle_it 1.158 r_scbond_it 1.032 r_scbond_other 1.032 r_mcbond_it 0.69 r_mcbond_other 0.678 r_nbd_refined 0.204 r_nbd_other 0.2 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.159 r_xyhbond_nbd_refined 0.159 r_symmetry_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.104 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.076 r_metal_ion_refined 0.053 r_chiral_restr_other 0.036 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2945 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing