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Structure of E37A BlaC from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 0.1 M sodium acetate, 0.2 M magnesium chloride, 20 % w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 1.94 36.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.56 α = 90 b = 54.739 β = 95 c = 54.509 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 PILATUS3 2M 2018-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.5 54.3 91.5 0.023 0.999 10.2 2.5 33194
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 97 0.358 0.768 1.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2GDN 1.5 54.36 31487 1688 91.37 0.12703 0.12456 0.17622 0.1896 RANDOM 20.396
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] 1.15 -0.35 -1.91 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.337 r_dihedral_angle_4_deg 18.815 r_dihedral_angle_3_deg 11.343 r_dihedral_angle_1_deg 6.604 r_long_range_B_refined 3.389 r_long_range_B_other 3.352 r_scangle_other 3.324 r_rigid_bond_restr 2.734 r_scbond_it 2.71 r_scbond_other 2.693
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.337 r_dihedral_angle_4_deg 18.815 r_dihedral_angle_3_deg 11.343 r_dihedral_angle_1_deg 6.604 r_long_range_B_refined 3.389 r_long_range_B_other 3.352 r_scangle_other 3.324 r_rigid_bond_restr 2.734 r_scbond_it 2.71 r_scbond_other 2.693 r_mcangle_other 2.34 r_mcangle_it 2.336 r_mcbond_it 1.936 r_mcbond_other 1.927 r_angle_refined_deg 1.772 r_angle_other_deg 1.603 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2004 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing