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Crystal structure of Mycoibacterium tuberculosis Rv2983 in complex with PEP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BWG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 30% PEG 1500, 3% MPD, 0.2 M MgSO4, 0.1 M sodium acetate pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.15 42.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.17 α = 90 b = 110.441 β = 90 c = 165.906 γ = 90
Symmetry Space Group C 2 2 21
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 ADSC QUANTUM 210r 2014-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95370 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.18 82.95 100 0.998 14.5 14.7 32157
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.25 0.376 1 13.2
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 6BWG 2.18 46.89 30620 1501 99.91 0.22168 0.21864 0.2275 0.28101 0.2851 RANDOM 48.101
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] -0.43 1.5 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.779 r_dihedral_angle_4_deg 21.955 r_dihedral_angle_3_deg 14.967 r_long_range_B_other 10.241 r_long_range_B_refined 10.23 r_scangle_other 7.847 r_dihedral_angle_1_deg 7.144 r_mcangle_it 6.979 r_mcangle_other 6.979 r_scbond_it 5.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.779 r_dihedral_angle_4_deg 21.955 r_dihedral_angle_3_deg 14.967 r_long_range_B_other 10.241 r_long_range_B_refined 10.23 r_scangle_other 7.847 r_dihedral_angle_1_deg 7.144 r_mcangle_it 6.979 r_mcangle_other 6.979 r_scbond_it 5.449 r_scbond_other 5.426 r_mcbond_it 4.881 r_mcbond_other 4.879 r_angle_refined_deg 1.709 r_angle_other_deg 0.948 r_chiral_restr 0.076 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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 4385 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing