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Crystal structure of N109P 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, 20 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.16 43.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.5 α = 90.95 b = 68.05 β = 90.47 c = 75.35 γ = 91.45
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 2020-02-17 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 1.89 35.49 93.7 0.861 1.28 2.1 48293
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 1.89 2.03 0.702
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 1.89 35.49 45947 2345 85.31 0.207 0.2041 0.2101 0.264 0.2671 RANDOM 12.344
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] -0.34 0.63 3.66 3.82 -0.35 -3.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.553 r_dihedral_angle_4_deg 21.603 r_dihedral_angle_3_deg 17.556 r_dihedral_angle_1_deg 7.705 r_angle_refined_deg 1.624 r_angle_other_deg 1.27 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.553 r_dihedral_angle_4_deg 21.603 r_dihedral_angle_3_deg 17.556 r_dihedral_angle_1_deg 7.705 r_angle_refined_deg 1.624 r_angle_other_deg 1.27 r_chiral_restr 0.075 r_bond_refined_d 0.008 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 5668 Nucleic Acid Atoms Solvent Atoms 585 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing