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Crystal Structure of H178N mutant of Glyceraldehyde-3-phosphate-dehydrogenase 1 (GAPDH 1) from Staphylococcus aureus MRSA252 complexed with NAD at 2.0 angstrom resolution.
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 8.2 277 0.1M Tris-HCl, pH 8.2, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.18 43.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.849 α = 90 b = 105.945 β = 108.343 c = 91.473 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 2009-05-05 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 86.82 95.3 0.064 9.9 3.73 80071 30.5
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 2.07 92.4 0.375 2.5 3.63 7739
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 29.06 80066 4003 95.24 0.199 0.197 0.2096 0.242 0.2503 RANDOM 32.455
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] 2.55 -0.92 -1.89 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.569 r_dihedral_angle_4_deg 21.547 r_dihedral_angle_3_deg 14.235 r_dihedral_angle_1_deg 5.975 r_scangle_it 2.452 r_scbond_it 1.538 r_angle_refined_deg 1.325 r_mcangle_it 0.915 r_mcbond_it 0.497 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.569 r_dihedral_angle_4_deg 21.547 r_dihedral_angle_3_deg 14.235 r_dihedral_angle_1_deg 5.975 r_scangle_it 2.452 r_scbond_it 1.538 r_angle_refined_deg 1.325 r_mcangle_it 0.915 r_mcbond_it 0.497 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10142 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms 182
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection d*TREK data reduction MOLREP phasing