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GMPK in complex with GDP and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LVG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 35% PEG4000, 0.1 M ammonium acetate, 0.1 M trisodium citrate, pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.1 41.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.278 α = 72.09 b = 44.478 β = 84.05 c = 67.445 γ = 75.87
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 PILATUS3 6M 2023-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
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 2.65 41.24 95.2 0.053 0.066 0.039 0.997 9.6 2.5 9883
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 2.65 2.78 95.4 0.228 0.287 0.171 0.922 2.6
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 1LVG 2.65 24.39 2.01 9875 547 95.27 0.2146 0.2116 0.2151 0.2661 0.2614
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 13.686 f_angle_d 0.652 f_chiral_restr 0.042 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2775 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 95
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction MOLREP phasing