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Crystal structure of Staphylococcus Aureus triosephosphate isomerase complexed with glycerol-3-phosphate
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 TRI-SODIUM CITRATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.54 51.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.1 α = 90 b = 81.1 β = 90 c = 174.6 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 2010-09-24 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 2.149 73.553 98.7 0.102 19.5 13 32236 24.5
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 2.15 2.26 91.7 0.439 0.439 1.8 11.2
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 2.15 20 32120 1628 98.9 0.183 0.181 0.194 0.223 0.2337 RANDOM 28.64
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] 1.17 1.17 -2.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.983 r_dihedral_angle_4_deg 14.757 r_dihedral_angle_3_deg 12.972 r_dihedral_angle_1_deg 5.088 r_scangle_it 4.678 r_scbond_it 2.727 r_angle_refined_deg 1.089 r_mcangle_it 0.881 r_mcbond_it 0.424 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.983 r_dihedral_angle_4_deg 14.757 r_dihedral_angle_3_deg 12.972 r_dihedral_angle_1_deg 5.088 r_scangle_it 4.678 r_scbond_it 2.727 r_angle_refined_deg 1.089 r_mcangle_it 0.881 r_mcbond_it 0.424 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3815 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 33
Software Software Software Name Purpose StructureStudio data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling