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High resolution crystal structure of LpqH from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZJM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 298 0.2M Ammonium sulphate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.85 33.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.9 α = 90 b = 78.51 β = 107.34 c = 42.18 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2021-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.258 28.557 99.1 0.061 0.067 0.078 0.047 0.997 10.1 4.5 49917
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.258 1.28 98 0.502 0.58 0.649 0.407 0.811
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4ZJM 1.258 28.557 49888 2464 99.106 0.145 0.1429 0.1779 0.2015 19.54
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] 2.045 0.358 -1.291 -0.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 51.07 r_dihedral_angle_3_deg 13.052 r_rigid_bond_restr 12.016 r_dihedral_angle_1_deg 6.742 r_scangle_it 5.824 r_scangle_other 5.821 r_lrange_it 5.529 r_lrange_other 5.515 r_scbond_it 4.727 r_scbond_other 4.723
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 51.07 r_dihedral_angle_3_deg 13.052 r_rigid_bond_restr 12.016 r_dihedral_angle_1_deg 6.742 r_scangle_it 5.824 r_scangle_other 5.821 r_lrange_it 5.529 r_lrange_other 5.515 r_scbond_it 4.727 r_scbond_other 4.723 r_mcangle_it 4.433 r_mcangle_other 4.433 r_mcbond_it 3.516 r_mcbond_other 3.514 r_angle_refined_deg 2.402 r_angle_other_deg 1.706 r_symmetry_nbd_refined 0.227 r_nbd_other 0.218 r_symmetry_nbd_other 0.2 r_nbd_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.117 r_symmetry_nbtor_other 0.093 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d 0.006 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1527 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing