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Crystal structure of 450-451_deletion mutant of FGAM Synthetase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 2M Ammonium Sulphate
Crystal Properties Matthews coefficient Solvent content 3.1 60.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.151 α = 90 b = 147.151 β = 90 c = 141.346 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2018-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.9 50 100 0.035 27.06 9.3 136288
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 0.172
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 1T3T 1.9 48.17 129371 6856 99.81 0.12709 0.12542 0.1386 0.15864 0.1675 RANDOM 19.637
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 r_dihedral_angle_2_deg 36.417 r_dihedral_angle_4_deg 18.211 r_dihedral_angle_3_deg 14.125 r_long_range_B_refined 7.575 r_long_range_B_other 7.276 r_dihedral_angle_1_deg 6.583 r_scangle_other 4.77 r_scbond_it 3.328 r_scbond_other 3.325 r_mcangle_it 2.461
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.417 r_dihedral_angle_4_deg 18.211 r_dihedral_angle_3_deg 14.125 r_long_range_B_refined 7.575 r_long_range_B_other 7.276 r_dihedral_angle_1_deg 6.583 r_scangle_other 4.77 r_scbond_it 3.328 r_scbond_other 3.325 r_mcangle_it 2.461 r_mcangle_other 2.461 r_angle_refined_deg 2.097 r_mcbond_it 1.868 r_mcbond_other 1.865 r_angle_other_deg 1.117 r_chiral_restr 0.131 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 9913 Nucleic Acid Atoms Solvent Atoms 1358 Heterogen Atoms 267
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing