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Crystal structure of D110G mutant of GATase subunit of Methanocaldococcus jannaschii GMP synthetase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7D40
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.6 277 100 mM Sodium acetate, pH 5.6, 10 % PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.27 45.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.18 α = 90 b = 66.65 β = 90 c = 79.18 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 277 IMAGE PLATE MAR scanner 345 mm plate 2017-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.29 50.99 89.3 0.97 4.02 4.7 8066
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.41 0.881
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7D40 2.29 50.99 7632 417 88.64 0.2141 0.2102 0.2151 0.2873 0.295 RANDOM 17.09
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] -0.47 -0.8 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.162 r_dihedral_angle_4_deg 27.959 r_dihedral_angle_3_deg 16.649 r_dihedral_angle_1_deg 7.388 r_angle_refined_deg 1.605 r_angle_other_deg 1.256 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.162 r_dihedral_angle_4_deg 27.959 r_dihedral_angle_3_deg 16.649 r_dihedral_angle_1_deg 7.388 r_angle_refined_deg 1.605 r_angle_other_deg 1.256 r_chiral_restr 0.07 r_bond_refined_d 0.009 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 1421 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing