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Structure of D172N 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 6.5 293 0.1 M MES, 0.1 M Imidazole, 30% EDO_8K, 0.09 M halogens (Sodium Fluoride, Sodium Bromide, Sodium Iodide)
Crystal Properties Matthews coefficient Solvent content 2.04 39.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.028 α = 90 b = 54.469 β = 90 c = 78.78 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER X 16M 2019-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00 SLS X06SA
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 1.4 44.8 98 0.041 0.997 9.3 3 45377
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 1.4 1.42 0.524 0.707 1.8 2.8
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 2GDN 1.4 44.84 43191 2145 97.44 0.13634 0.13453 0.1361 0.17229 0.1439 RANDOM
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] -0.39 1.07 -0.68
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 5.287 r_scangle_other 3.031 r_long_range_B_refined 2.773 r_long_range_B_other 2.704 r_scbond_it 2.655 r_scbond_other 2.654 r_mcangle_other 1.786 r_mcangle_it 1.783 r_mcbond_it 1.387 r_mcbond_other 1.374
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 5.287 r_scangle_other 3.031 r_long_range_B_refined 2.773 r_long_range_B_other 2.704 r_scbond_it 2.655 r_scbond_other 2.654 r_mcangle_other 1.786 r_mcangle_it 1.783 r_mcbond_it 1.387 r_mcbond_other 1.374 r_bond_refined_d r_bond_other_d r_angle_refined_deg r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_chiral_restr r_gen_planes_refined r_gen_planes_other 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 1995 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing