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Crystal structure of Rv0802c from Mycobacterium tuberculosis in Complex with Succinyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VZY PDB ENTRY 2VZY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 PROTEIN AT 8 MG/ML IN 20 MM TEA PH 8.5, 100 MM AMMONIUM SULFATE, 1 MM EDTA, 1 MM DTT, 2 MM COA, 4 MM SUCCOA CRYSTALLIZED IN 1 M LICL, 100 MM HEPES PH 7.0. CRYOPROTECTED IN PRECIPITANT SOLUTION PLUS 20 MM SUCCOA AND 20% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 3.03 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.165 α = 90 b = 135.172 β = 90 c = 164.077 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 IMAGE PLATE RIGAKU IMAGE PLATE OSMIC BLUE CONFOCAL 2004-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 2.3 104 95.9 0.06 15.3 3.5 53759
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 2.3 2.38 92.8 0.2 4.8 3
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 2VZY 2.3 104.26 51029 2730 95.8 0.172 0.169 0.1714 0.222 0.2229 RANDOM 19.81
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] 0.33 1.26 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.199 r_dihedral_angle_4_deg 16.542 r_dihedral_angle_3_deg 14.568 r_dihedral_angle_1_deg 5.914 r_scangle_it 3.623 r_scbond_it 2.247 r_angle_refined_deg 1.684 r_mcangle_it 1.321 r_mcbond_it 0.779 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.199 r_dihedral_angle_4_deg 16.542 r_dihedral_angle_3_deg 14.568 r_dihedral_angle_1_deg 5.914 r_scangle_it 3.623 r_scbond_it 2.247 r_angle_refined_deg 1.684 r_mcangle_it 1.321 r_mcbond_it 0.779 r_nbtor_refined 0.304 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.188 r_symmetry_hbond_refined 0.155 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6763 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms 220
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing