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Anthranilate phosphoribosyltransferase from Thermococcus kodakaraensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NOE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 0.2 M sodium nitrate, 0.1 M Bis-Tris propane buffer (pH 8.5), 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.605 α = 90 b = 81.389 β = 90 c = 179.392 γ = 90
Symmetry Space Group P 2 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 100 PIXEL DECTRIS PILATUS3 S 6M 2016-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.03320 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.42 48.19 99.8 0.152 0.997 9.6 7 24674 59
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 2.42 2.5 99 1.32 0.467 1.4 7.2
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 5NOE 2.42 48.19 23378 1230 99.7 0.19758 0.19454 0.2007 0.25451 0.2505 RANDOM 55.471
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] -0.71 1.51 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.226 r_dihedral_angle_3_deg 16.665 r_dihedral_angle_4_deg 16.204 r_long_range_B_other 16.05 r_long_range_B_refined 16.042 r_scangle_other 12.714 r_mcangle_it 10.242 r_mcangle_other 10.242 r_scbond_it 8.854 r_scbond_other 8.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.226 r_dihedral_angle_3_deg 16.665 r_dihedral_angle_4_deg 16.204 r_long_range_B_other 16.05 r_long_range_B_refined 16.042 r_scangle_other 12.714 r_mcangle_it 10.242 r_mcangle_other 10.242 r_scbond_it 8.854 r_scbond_other 8.847 r_mcbond_it 7.205 r_mcbond_other 7.203 r_dihedral_angle_1_deg 6.355 r_angle_refined_deg 1.413 r_angle_other_deg 1.017 r_chiral_restr 0.107 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 4824 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing