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Crystal Structure of D464A 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 3.07 59.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.461 α = 90 b = 146.461 β = 90 c = 141.54 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++ 2014-12-12 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 2.1 50 100 0.048 24.7 5.6 100187
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 2.1 2.14 0.185
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 2.1 32.52 95120 5004 99.95 0.14753 0.14534 0.1584 0.18891 0.1943 RANDOM 27.925
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.637 r_dihedral_angle_4_deg 19.029 r_dihedral_angle_3_deg 14.985 r_long_range_B_refined 8.624 r_long_range_B_other 8.623 r_dihedral_angle_1_deg 6.902 r_scangle_other 5.107 r_scbond_it 3.486 r_scbond_other 3.486 r_mcangle_it 3.448
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.637 r_dihedral_angle_4_deg 19.029 r_dihedral_angle_3_deg 14.985 r_long_range_B_refined 8.624 r_long_range_B_other 8.623 r_dihedral_angle_1_deg 6.902 r_scangle_other 5.107 r_scbond_it 3.486 r_scbond_other 3.486 r_mcangle_it 3.448 r_mcangle_other 3.448 r_mcbond_it 2.457 r_mcbond_other 2.456 r_angle_refined_deg 1.944 r_angle_other_deg 1.07 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 9878 Nucleic Acid Atoms Solvent Atoms 855 Heterogen Atoms 141
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing