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Crystal structure of CotA native enzyme, PH8.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GSK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 30-42%(v/v) ethylene glycol, 100mM NaCl, 25mM Tris-HCl
Crystal Properties Matthews coefficient Solvent content 3.48 64.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.897 α = 90 b = 101.897 β = 90 c = 136.162 γ = 120
Symmetry Space Group P 31 2 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 CCD MARMOSAIC 325 mm CCD 2014-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 1.000 BSRF 3W1A
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 1.96 30 99.2 0.074 26.2 7.4 58806
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 1.96 2.03 97.9 0.234 8.4 6.8
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 1gsk 1.96 29.97 55800 2982 99.17 0.15511 0.15359 0.165 0.1838 0.1934 RANDOM 23.797
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] 0.01 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.72 r_dihedral_angle_4_deg 18.815 r_dihedral_angle_3_deg 12.263 r_long_range_B_refined 6.767 r_dihedral_angle_1_deg 6.728 r_long_range_B_other 6.242 r_scangle_other 3.97 r_mcangle_it 2.737 r_mcangle_other 2.737 r_scbond_it 2.534
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.72 r_dihedral_angle_4_deg 18.815 r_dihedral_angle_3_deg 12.263 r_long_range_B_refined 6.767 r_dihedral_angle_1_deg 6.728 r_long_range_B_other 6.242 r_scangle_other 3.97 r_mcangle_it 2.737 r_mcangle_other 2.737 r_scbond_it 2.534 r_scbond_other 2.533 r_mcbond_it 1.786 r_mcbond_other 1.785 r_angle_refined_deg 1.553 r_angle_other_deg 0.792 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 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 4054 Nucleic Acid Atoms Solvent Atoms 530 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing