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Crystal structure of Mycobacterium tuberculosis Rv0376c homologue from Mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WE7 PDB ENTRY 2WE7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1 M CITRATE PH 4.8, 17% PEG 8000, 0.2 M AMMONIUM ACETATE AND 4% ETHANOL BY MICRO-SEEDING.
Crystal Properties Matthews coefficient Solvent content 2.67 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.208 α = 90 b = 101.208 β = 90 c = 316.669 γ = 120
Symmetry Space Group P 63 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 294 CCD ADSC CCD MIRRORS 2007-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A PAL/PLS 4A
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 2.16 50 97.9 0.11 25.6 18.7 51359
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 2.16 2.24 83.6 0.1 2.05 3.4
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 2WE7 2.3 33.73 41413 2223 99.8 0.201 0.199 0.2041 0.251 0.2559 RANDOM 54.81
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] -0.06 -0.03 -0.06 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.387 r_dihedral_angle_4_deg 21.58 r_dihedral_angle_3_deg 18.435 r_scangle_it 7.056 r_dihedral_angle_1_deg 5.85 r_scbond_it 4.828 r_mcangle_it 2.906 r_mcbond_it 1.709 r_angle_refined_deg 1.289 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.387 r_dihedral_angle_4_deg 21.58 r_dihedral_angle_3_deg 18.435 r_scangle_it 7.056 r_dihedral_angle_1_deg 5.85 r_scbond_it 4.828 r_mcangle_it 2.906 r_mcbond_it 1.709 r_angle_refined_deg 1.289 r_nbtor_refined 0.301 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.189 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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 5017 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement DENZO data reduction HKL-2000 data scaling AMoRE phasing