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Class A beta-lactamase from Mycobacterium abscessus
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, HANGING DROP 6.5 293 0.1 M sodium acetate, 0.1 MES (pH 6.5), 32% polyethylene glycol monomethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 2.12 41.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.49 α = 90 b = 65.21 β = 90.94 c = 107.42 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 PSI PILATUS 6M 2013-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9801 SOLEIL PROXIMA 1
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 1.4 41.5 94.6 0.066 11.29 3.3 93890
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 1.4 1.48 73.2 0.669 1.34 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 2GDN 1.4 41.45 89195 4695 94.6 0.14447 0.14307 0.1427 0.1712 0.1709 RANDOM 18.543
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] -0.96 0.68 -0.36 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.002 r_dihedral_angle_4_deg 17.086 r_dihedral_angle_3_deg 11.295 r_long_range_B_refined 6.189 r_long_range_B_other 5.95 r_dihedral_angle_1_deg 5.602 r_scangle_other 4.85 r_scbond_it 3.32 r_scbond_other 3.309 r_mcangle_it 2.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.002 r_dihedral_angle_4_deg 17.086 r_dihedral_angle_3_deg 11.295 r_long_range_B_refined 6.189 r_long_range_B_other 5.95 r_dihedral_angle_1_deg 5.602 r_scangle_other 4.85 r_scbond_it 3.32 r_scbond_other 3.309 r_mcangle_it 2.123 r_mcangle_other 2.123 r_angle_refined_deg 2.027 r_mcbond_it 1.617 r_mcbond_other 1.496 r_angle_other_deg 0.948 r_chiral_restr 0.133 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 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 3952 Nucleic Acid Atoms Solvent Atoms 469 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing