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Crystal Structure of Thioacyl-Glyceraldehyde-3-phosphate dehydrogenase 1(GAPDH 1) from methicillin resistant Staphylococcus aureus MRSA252
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H48
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1M Tris-HCl pH 8.5, 32% (w/v) PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.09 41.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.057 α = 90 b = 103.025 β = 109.4 c = 90.303 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 Varimax mirrors 2009-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.793 85.178 99.2 0.134 3.8 29489 29489 46
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 2.79 2.94 96.9 0.497 2.7 3.7 4196
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 3H48 2.8 20 29373 1492 99.82 0.184 0.181 0.1924 0.241 0.2485 RANDOM 37.376
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] -0.98 -1.33 2.33 -2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.147 r_dihedral_angle_4_deg 20.644 r_dihedral_angle_3_deg 17.302 r_scangle_it 6.637 r_dihedral_angle_1_deg 6.242 r_scbond_it 3.722 r_angle_refined_deg 1.432 r_mcangle_it 1.31 r_mcbond_it 0.626 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.147 r_dihedral_angle_4_deg 20.644 r_dihedral_angle_3_deg 17.302 r_scangle_it 6.637 r_dihedral_angle_1_deg 6.242 r_scbond_it 3.722 r_angle_refined_deg 1.432 r_mcangle_it 1.31 r_mcbond_it 0.626 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10124 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 61
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction MOLREP phasing