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Crystal structure of Staphylococcus Aureus triosephosphate isomerase complexed with 3-phosphoglyceric acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M9Y PDB ENTRY 3M9Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 1.6M TRISODIUM CITRATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 50.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.583 α = 90 b = 80.583 β = 90 c = 174.042 γ = 90
Symmetry Space Group P 43 21 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++ MIRROR 2010-12-07 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 Sym 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 2.247 73.125 99.6 0.081 15.1 5.8 28110 35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.37 98.7 0.466 0.466 1.6 5.7
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 3M9Y 2.25 29.56 26625 1412 99.6 0.209 0.206 0.2219 0.248 0.2573 RANDOM 34.53
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] 1.35 1.35 -2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.031 r_dihedral_angle_3_deg 13.477 r_dihedral_angle_4_deg 8.591 r_dihedral_angle_1_deg 4.931 r_scangle_it 4.343 r_scbond_it 2.411 r_angle_refined_deg 1.056 r_mcangle_it 0.921 r_mcbond_it 0.449 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.031 r_dihedral_angle_3_deg 13.477 r_dihedral_angle_4_deg 8.591 r_dihedral_angle_1_deg 4.931 r_scangle_it 4.343 r_scbond_it 2.411 r_angle_refined_deg 1.056 r_mcangle_it 0.921 r_mcbond_it 0.449 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3809 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 31
Software Software Software Name Purpose StructureStudio data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling