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Magnesium soaked into 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 7.5 291 0.2 M imidazole-malate, 15% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.78 59.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.368 α = 90 b = 91.201 β = 90 c = 119.865 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 110 IMAGE PLATE MAR scanner 345 mm plate 2015-05-31 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 2.008 34 99.5 0.138 20.6 14.4 58525 -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 2.008 2.06 92.4 1.364 2.3 12.9
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 2.009 33.088 1.33 57253 2820 97.54 0.2184 0.2166 0.2191 0.2529 0.253 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 11.486 f_angle_d 0.714 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 5025 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement Blu-Ice data collection