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Structure of Rv2140c, a phosphatidyl-ethanolamine binding protein from Mycobacterium tuberculosis in complex with sulphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BEF PDB ENTRY 4BEF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M TRIS PH 8.0, 2.4 M AMMONIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.118 α = 90 b = 62.118 β = 90 c = 181.8 γ = 90
Symmetry Space Group P 41 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 MAR scanner 345 mm plate M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 1.41 28.01 97.9 0.05 7.86 5.32 67729
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.41 1.49 87.2 0.27 2.81 5.23
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 FREE R-VALUE PDB ENTRY 4BEF 1.42 27.248 67658 3427 99.189 0.151 0.1491 0.1469 0.1949 0.1928 RANDOM 15.055
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] 0.457 0.457 -0.913
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.356 r_sphericity_free 23.027 r_dihedral_angle_4_deg 17.22 r_dihedral_angle_3_deg 11.078 r_sphericity_bonded 9.082 r_rigid_bond_restr 7.082 r_dihedral_angle_1_deg 6.562 r_angle_refined_deg 2.017 r_chiral_restr 0.148 r_bond_refined_d 0.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.356 r_sphericity_free 23.027 r_dihedral_angle_4_deg 17.22 r_dihedral_angle_3_deg 11.078 r_sphericity_bonded 9.082 r_rigid_bond_restr 7.082 r_dihedral_angle_1_deg 6.562 r_angle_refined_deg 2.017 r_chiral_restr 0.148 r_bond_refined_d 0.021 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2637 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement PHASER phasing