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Crystal Structure of a Pantothenate Synthetase from M. tuberculosis in complex with a reaction intermediate, pantoyl adenylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MOP PDB entry 1MOP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 PEG3000, lithium sulfate, manganese chloride, imidazole, ethanol, glycerol, ATP, sodium D-pantoate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.258 α = 90 b = 70.861 β = 99.34 c = 81.822 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU RAXIS IV++ mirrors 2002-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-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 2 50 94.3 0.125 0.125 10.3 4 34665 34665 -3 14.7
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 2 2.07 91.4 0.426 0.426 2.8 3.8 3308
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 rigid body refinement into new data THROUGHOUT PDB entry 1MOP 2 19.82 34619 34619 2787 94 0.182 0.182 0.1791 0.218 0.2154 RANDOM 21.8
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] 1.51 -2.29 2.63 -4.14
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.8 c_scangle_it 3.81 c_scbond_it 2.85 c_mcangle_it 2.54 c_mcbond_it 1.88 c_angle_deg 1.6 c_improper_angle_d 1.09 c_bond_d 0.014 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.8 c_scangle_it 3.81 c_scbond_it 2.85 c_mcangle_it 2.54 c_mcbond_it 1.88 c_angle_deg 1.6 c_improper_angle_d 1.09 c_bond_d 0.014 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4237 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 101
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing