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Crystal structure of Triosephosphate isomerase from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YYA pdb entry 1yya, modified with the ccp4 program chainsaw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 JCSG+ A3: 200MM (NH4)2H CITRATE, 20% PEG 3350, MYTUD.00317.A AT 30MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.31 46.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.12 α = 90 b = 55.76 β = 104.01 c = 76.42 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 100 IMAGE PLATE MAR scanner 300 mm plate 2009-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
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 1.55 74.15 99.5 0.064 13.89 3.7 79018 78636 -3 22.37
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 1.55 1.59 98.2 0.515 2.5 3.4 5789
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR THROUGHOUT pdb entry 1yya, modified with the ccp4 program chainsaw 1.55 20 78636 78636 3950 99.5 0.145 0.143 0.1552 0.169 0.1796 RANDOM 14.07
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] -0.16 -0.49 0.99 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.095 r_dihedral_angle_4_deg 15.264 r_dihedral_angle_3_deg 11.636 r_dihedral_angle_1_deg 5.633 r_scangle_it 4.348 r_scbond_it 2.705 r_mcangle_it 1.768 r_angle_refined_deg 1.7 r_mcbond_it 1.053 r_angle_other_deg 1.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.095 r_dihedral_angle_4_deg 15.264 r_dihedral_angle_3_deg 11.636 r_dihedral_angle_1_deg 5.633 r_scangle_it 4.348 r_scbond_it 2.705 r_mcangle_it 1.768 r_angle_refined_deg 1.7 r_mcbond_it 1.053 r_angle_other_deg 1.022 r_mcbond_other 0.328 r_chiral_restr 0.101 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3778 Nucleic Acid Atoms Solvent Atoms 650 Heterogen Atoms 18
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling