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Crystal structure of C151S mutant of Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH 1)from methicillin resistant Staphylococcus aureus MRSA252 complexed with NAD and G3P
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 8.2 298 0.1 (M) Tris-HCl, pH 8.2, 26% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.519 α = 90 b = 104.49 β = 108.03 c = 91.192 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 2009-06-22 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 2.5 86.71 98.8 0.084 9.7 3.73 41759 54.2
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 2.5 2.59 97.7 0.344 3.2 3.71 4116
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 2.5 21.35 41750 2100 98.56 0.19 0.187 0.1981 0.238 0.2451 RANDOM 39.086
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] -0.85 -0.44 2.53 -1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.865 r_dihedral_angle_4_deg 25.182 r_dihedral_angle_3_deg 15.761 r_dihedral_angle_1_deg 6.562 r_scangle_it 6.425 r_scbond_it 3.809 r_angle_refined_deg 1.571 r_mcangle_it 1.416 r_mcbond_it 0.661 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.865 r_dihedral_angle_4_deg 25.182 r_dihedral_angle_3_deg 15.761 r_dihedral_angle_1_deg 6.562 r_scangle_it 6.425 r_scbond_it 3.809 r_angle_refined_deg 1.571 r_mcangle_it 1.416 r_mcbond_it 0.661 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10124 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 220
Software Software Software Name Purpose d*TREK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection d*TREK data reduction