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Crystal structure of serine bound D-3-phosphoglycerate dehydrogenase from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YGY
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 3.94 68.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.192 α = 90 b = 165.192 β = 90 c = 218.894 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 100 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-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 2.7 46.57 99.2 0.037 19.2 20.8 48518
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 2.7 2.8 99.9 0.42 2.8 19.5
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 1YGY 2.7 46.57 46059 2452 99.2 0.22433 0.22227 0.21 0.26324 0.2511 RANDOM 67.598
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] 5.8 2.9 5.8 -8.7
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.765 r_bond_refined_d 0.019 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_chiral_restr r_gen_planes_refined r_nbd_refined r_nbtor_refined
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.765 r_bond_refined_d 0.019 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_chiral_restr r_gen_planes_refined r_nbd_refined r_nbtor_refined r_xyhbond_nbd_refined r_symmetry_vdw_refined r_symmetry_hbond_refined r_mcbond_it r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7640 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling XFIT data reduction