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DHAP bound Leptospira Interrogans Triosephosphate Isomerase (LiTIM)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X22
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 293 16% PEG 8000, 1mM Ammonium sulfate, 10mM EDTA, 1mM Sodium azide, 100mM BIS/TRIS
Crystal Properties Matthews coefficient Solvent content 3.23 61.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.758 α = 90 b = 103.758 β = 90 c = 113.505 γ = 120
Symmetry Space Group P 32 2 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 CCD MARMOSAIC 225 mm CCD 2014-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95372 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.87 56.75 92.7 13.3 11.8 58862 54809 22.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.97
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 4X22 1.87 56.75 52007 2593 92.76 0.17295 0.17112 0.1803 0.2107 0.2145 RANDOM 27.82
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.676 r_dihedral_angle_4_deg 13.87 r_dihedral_angle_3_deg 12.606 r_dihedral_angle_1_deg 6.229 r_long_range_B_other 5.637 r_long_range_B_refined 5.636 r_scangle_other 4.402 r_scbond_it 3.208 r_scbond_other 3.206 r_mcangle_other 3.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.676 r_dihedral_angle_4_deg 13.87 r_dihedral_angle_3_deg 12.606 r_dihedral_angle_1_deg 6.229 r_long_range_B_other 5.637 r_long_range_B_refined 5.636 r_scangle_other 4.402 r_scbond_it 3.208 r_scbond_other 3.206 r_mcangle_other 3.187 r_mcangle_it 3.182 r_mcbond_it 2.578 r_mcbond_other 2.568 r_angle_refined_deg 2.015 r_angle_other_deg 0.942 r_chiral_restr 0.131 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 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 3739 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing