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Crystal Structure of the Mycobacterium tuberculosis Indole-3-glycerol phosphate synthase (TrpC) in apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VC4 PDB entry 1VC4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 298 0.1M Sodium acetate trihydrate, 2.0M Ammonium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.05 40.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.069 α = 90 b = 53.505 β = 90 c = 87.826 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 CCD MARMOSAIC 300 mm CCD mirrors 2009-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97933 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.29 50 99.9 0.067 0.067 15.6 13.8 59034 59034 12.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.29 1.31 100 0.424 0.424 9.54 12.8 2905
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 1VC4 1.29 33.45 58786 58786 2980 99.75 0.1641 0.1641 0.1632 0.171 0.1809 0.1893 RANDOM 16.1591
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.697 r_dihedral_angle_4_deg 15.172 r_dihedral_angle_3_deg 11.13 r_dihedral_angle_1_deg 4.835 r_sphericity_free 3.079 r_scangle_it 2.709 r_scbond_it 1.8 r_rigid_bond_restr 1.729 r_sphericity_bonded 1.619 r_mcangle_it 1.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.697 r_dihedral_angle_4_deg 15.172 r_dihedral_angle_3_deg 11.13 r_dihedral_angle_1_deg 4.835 r_sphericity_free 3.079 r_scangle_it 2.709 r_scbond_it 1.8 r_rigid_bond_restr 1.729 r_sphericity_bonded 1.619 r_mcangle_it 1.225 r_angle_refined_deg 1.097 r_angle_other_deg 0.858 r_mcbond_it 0.764 r_mcbond_other 0.268 r_nbd_refined 0.218 r_symmetry_vdw_other 0.205 r_nbd_other 0.195 r_symmetry_vdw_refined 0.17 r_nbtor_refined 0.164 r_symmetry_hbond_refined 0.126 r_xyhbond_nbd_refined 0.103 r_nbtor_other 0.086 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1806 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 5
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction