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Crystal Structure of Triosephosphate Isomerase from Brucella melitensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KXQ PDB ENTRY 3kxq
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 MCSG1a11: 10% PEG4K, 0.2M MgCl2, 0.1M Mes pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.35 47.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.91 α = 104.57 b = 60.6 β = 99.46 c = 86.17 γ = 90.31
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 2013-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
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 2.1 50 98.1 0.09 12.1 3.94 58506 57366 15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 96.9 0.52 2.7 3.97 4227
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 3kxq 2.1 50 54462 2904 98.13 0.1792 0.17643 0.1835 0.23023 0.2332 RANDOM 29.563
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] -0.02 0.18 0.99 -2.07 0.26 1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.705 r_dihedral_angle_4_deg 16.809 r_dihedral_angle_3_deg 13.435 r_dihedral_angle_1_deg 5.665 r_long_range_B_refined 5.251 r_long_range_B_other 5.143 r_scangle_other 2.987 r_mcangle_it 2.372 r_mcangle_other 2.372 r_scbond_it 1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.705 r_dihedral_angle_4_deg 16.809 r_dihedral_angle_3_deg 13.435 r_dihedral_angle_1_deg 5.665 r_long_range_B_refined 5.251 r_long_range_B_other 5.143 r_scangle_other 2.987 r_mcangle_it 2.372 r_mcangle_other 2.372 r_scbond_it 1.89 r_scbond_other 1.89 r_mcbond_it 1.577 r_mcbond_other 1.577 r_angle_refined_deg 1.532 r_angle_other_deg 0.814 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7070 Nucleic Acid Atoms Solvent Atoms 557 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling