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PRPP complexed with two Mn2+ in the active site of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QR9 PDB entry 3QR9 chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 0.2 M imidazole-malate, 9% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.25 45.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.178 α = 90 b = 78.481 β = 109.9 c = 100.446 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MAR scanner 345 mm plate 2015-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 25 94.6 0.062 13.1 2.8 38040 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 100 0.291 3.6 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE PDB entry 3QR9 chain A 2.1 24.556 1.33 37441 1742 93.06 0.2047 0.2023 0.2035 0.2539 0.2548 Random selection
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 f_dihedral_angle_d 10.574 f_angle_d 0.712 f_chiral_restr 0.027 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4952 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement XDS data scaling Aimless data scaling PHASER phasing REFMAC refinement Blu-Ice data collection XDS data reduction