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Crystal Structure of D-3-Phosphoglycerate dehydrogenase From Mycobacterium tuberculosis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 sodium potassium tartrate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.9 68.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.513 α = 90 b = 165.513 β = 90 c = 218.144 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 4 2003-12-14 M MAD 2 1 x-ray CCD ADSC QUANTUM 315 2004-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D 0.97937, 0.97961 APS 14-BM-D 2 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
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 2.3 50 99.7 0.095 24.7 14.3 78223
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 2.3 2.38 99.9 0.404 4.8 9.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.3 48.8 74263 3918 99.78 0.20715 0.20496 0.201 0.24853 0.2434 RANDOM 36.302
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] 2.72 1.36 2.72 -4.08
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 8.932 r_dihedral_angle_1_deg 7.202 r_scbond_it 6.574 r_mcangle_it 4.826 r_mcbond_it 3.183 r_angle_refined_deg 1.478 r_nbd_refined 0.255 r_symmetry_hbond_refined 0.254 r_symmetry_vdw_refined 0.246 r_xyhbond_nbd_refined 0.187
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 8.932 r_dihedral_angle_1_deg 7.202 r_scbond_it 6.574 r_mcangle_it 4.826 r_mcbond_it 3.183 r_angle_refined_deg 1.478 r_nbd_refined 0.255 r_symmetry_hbond_refined 0.254 r_symmetry_vdw_refined 0.246 r_xyhbond_nbd_refined 0.187 r_chiral_restr 0.114 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7672 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SHARP phasing