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Crystal structure of D110V/K151L 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 298 0.1M MES pH 6.5, 0.2M Ammonium sulfate, 30% PEG monomethyl ether 5000
Crystal Properties Matthews coefficient Solvent content 3.11 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.78 α = 90 b = 93.78 β = 90 c = 119.09 γ = 90
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 2022-04-26 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) R Merge 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 2.5 58 100 0.251 0.278 0.955 6.3 5.5 35659
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 100 0.5 0.532 3.3 5.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7D40 2.5 58 33977 1667 99.96 0.21124 0.20948 0.24685 0.2186 RANDOM 9.967
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] -0.28 -0.28 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.894 r_dihedral_angle_4_deg 20.005 r_dihedral_angle_3_deg 19.947 r_dihedral_angle_1_deg 6.531 r_long_range_B_refined 3.457 r_long_range_B_other 3.431 r_angle_other_deg 2.366 r_angle_refined_deg 1.628 r_scangle_other 1.527 r_mcangle_it 1.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.894 r_dihedral_angle_4_deg 20.005 r_dihedral_angle_3_deg 19.947 r_dihedral_angle_1_deg 6.531 r_long_range_B_refined 3.457 r_long_range_B_other 3.431 r_angle_other_deg 2.366 r_angle_refined_deg 1.628 r_scangle_other 1.527 r_mcangle_it 1.514 r_mcangle_other 1.514 r_scbond_it 0.959 r_scbond_other 0.941 r_mcbond_it 0.875 r_mcbond_other 0.875 r_chiral_restr 0.085 r_bond_other_d 0.036 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5768 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing