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Crystal structure of Staphylococcal GAPDH1 in a hexagonal space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K73 PDB ENTRY 3K73
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 22% PEG 400, 0.2M CaCl2, 0.1M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.48 50.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.389 α = 90 b = 155.389 β = 90 c = 317.849 γ = 120
Symmetry Space Group P 62 2 2
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++ 2011-09-25 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 3.19 29.742 99.6 0.315 13.8 38297 -3 17.228
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.19 3.39 99 0.733 0.751 5.35
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 PDB ENTRY 3K73 3.19 29.74 38297 1915 100 0.2059 0.2022 0.1903 0.277 0.2617 RANDOM 19.828
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] -1.77 -0.88 -1.77 2.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.934 r_dihedral_angle_4_deg 19.342 r_dihedral_angle_3_deg 15.637 r_dihedral_angle_1_deg 5.018 r_angle_refined_deg 0.995 r_mcangle_it 0.291 r_mcbond_it 0.163 r_scangle_it 0.122 r_chiral_restr 0.064 r_scbond_it 0.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.934 r_dihedral_angle_4_deg 19.342 r_dihedral_angle_3_deg 15.637 r_dihedral_angle_1_deg 5.018 r_angle_refined_deg 0.995 r_mcangle_it 0.291 r_mcbond_it 0.163 r_scangle_it 0.122 r_chiral_restr 0.064 r_scbond_it 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14999 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 308
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling