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Anthranilate phosphoribosyltransferase variant Ser121Ala from Saccharomyces cerevisiae with Mg bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DSM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 287 18 % MPEG 5000,
0.1 M HEPES pH7.0
Crystal Properties Matthews coefficient Solvent content 2.18 43.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.164 α = 90 b = 87.002 β = 90 c = 108.433 γ = 90
Symmetry Space Group P 21 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 6M 2020-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.95 50 100 0.09 0.025 32.2 13 55409
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 100 0.517 0.143 3.7 12.9
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 7DSM 1.95 46.06 52587 2726 99.9 0.1657 0.1635 0.2079 0.2132 RANDOM 29.652
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] -0.12 1.19 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.418 r_dihedral_angle_3_deg 15.902 r_dihedral_angle_4_deg 14.359 r_dihedral_angle_1_deg 6.323 r_angle_refined_deg 1.493 r_angle_other_deg 1.46 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.418 r_dihedral_angle_3_deg 15.902 r_dihedral_angle_4_deg 14.359 r_dihedral_angle_1_deg 6.323 r_angle_refined_deg 1.493 r_angle_other_deg 1.46 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5473 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing