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Crystal Structure of holo Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1) from methicillin resistant Staphylococcus aureus MRSA252 at 1.7 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HDG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 0.1M Tris-HCl, pH8.5, 20% (w/v)PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.13 42.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.18 α = 90 b = 104.874 β = 107.72 c = 91.191 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 2009-05-14 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 Merge I (Observed) Rrim I (All) 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 1.7 30.78 94.5 0.059 0.059 8.7 3.52 126584 38.7
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) 1.7 1.76 93.6 0.43 2.4 3.36 12506
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 1HDG 1.7 20 126514 6358 94.48 0.19 0.189 0.1984 0.221 0.2274 RANDOM 39.013
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] 0.37 -0.02 0.48 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.576 r_dihedral_angle_4_deg 18.274 r_dihedral_angle_3_deg 11.685 r_dihedral_angle_1_deg 5.406 r_scangle_it 3.23 r_scbond_it 1.844 r_angle_refined_deg 1.04 r_mcangle_it 0.658 r_mcbond_it 0.317 r_chiral_restr 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.576 r_dihedral_angle_4_deg 18.274 r_dihedral_angle_3_deg 11.685 r_dihedral_angle_1_deg 5.406 r_scangle_it 3.23 r_scbond_it 1.844 r_angle_refined_deg 1.04 r_mcangle_it 0.658 r_mcbond_it 0.317 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10152 Nucleic Acid Atoms Solvent Atoms 671 Heterogen Atoms 176
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection d*TREK data reduction MOLREP phasing