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The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis complexed with phenylalanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B7O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 20MM BTP, 150MM NACL, 0.5MM TCEP, 0.005%(V/V) THESIT, 0.2MM PEP, 0.1MM MNCL2, 0.1M NA HEPES, 0.8M NAK PHOSPHATE , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.96 68.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.65 α = 90 b = 204.65 β = 90 c = 66.61 γ = 120
Symmetry Space Group P 32 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 123 IMAGE PLATE RIGAKU RAXIS IV++ OSMIC BLUE MIRRORS 2005-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.542
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 3 39.6 97.2 0.164 5.6 2.63 31363 31363 36.2
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 3 3.077 97.2 0.344 3 2.68 31363
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2B7O 3 39.55 29566 1574 96.5 0.21517 0.21227 0.2167 0.2694 0.2726 RANDOM 32.676
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] 0.63 0.32 0.63 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.469 r_dihedral_angle_4_deg 15.204 r_dihedral_angle_3_deg 14.952 r_dihedral_angle_1_deg 5.488 r_scangle_it 5.143 r_scbond_it 3.124 r_mcangle_it 2.447 r_mcbond_it 1.333 r_angle_other_deg 1.27 r_angle_refined_deg 1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.469 r_dihedral_angle_4_deg 15.204 r_dihedral_angle_3_deg 14.952 r_dihedral_angle_1_deg 5.488 r_scangle_it 5.143 r_scbond_it 3.124 r_mcangle_it 2.447 r_mcbond_it 1.333 r_angle_other_deg 1.27 r_angle_refined_deg 1.16 r_mcbond_other 0.188 r_chiral_restr 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6756 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 85
Software Software Software Name Purpose CrystalClear data collection CCP4 model building REFMAC refinement d*TREK data reduction d*TREK data scaling CCP4 phasing