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Crystal Structure of apo Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1) from methicllin 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 Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.288 α = 90 b = 94.937 β = 105.73 c = 86.552 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 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 2.494 83.311 99.3 0.061 19.1 3.7 34746 34746 38
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 2.49 2.63 96.7 0.281 4.5 3.5 4921
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 MOLECULAR REPLACEMENT THROUGHOUT 3H48 2.5 20 34621 34621 354 99.89 0.188 0.187 0.2263 0.249 0.2748 RANDOM 40.942
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] 1.66 -0.62 -1.03 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.496 r_dihedral_angle_4_deg 25.01 r_dihedral_angle_3_deg 17.319 r_dihedral_angle_1_deg 7.012 r_scangle_it 6.45 r_scbond_it 3.808 r_angle_refined_deg 1.576 r_mcangle_it 1.441 r_mcbond_it 0.717 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.496 r_dihedral_angle_4_deg 25.01 r_dihedral_angle_3_deg 17.319 r_dihedral_angle_1_deg 7.012 r_scangle_it 6.45 r_scbond_it 3.808 r_angle_refined_deg 1.576 r_mcangle_it 1.441 r_mcbond_it 0.717 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10075 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 12
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction MOLREP phasing