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Crystal structure of CotA native enzyme in the acid condition, PH5.6
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 5.6 293 30-42%(v/v) ethylene glycol,100mM sodium citrate, pH 5.6
Crystal Properties Matthews coefficient Solvent content 3.46 64.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.73 α = 90 b = 101.73 β = 90 c = 135.572 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 MAR CCD 165 mm 2013-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 1.0000 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 2.3 29.4 100 0.097 12.2 3.7 36605
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 2.3 2.34 100 0.281 4.6 3.7
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 2.3 29.38 34656 1824 99.64 0.16041 0.15899 0.1672 0.18693 0.1932 RANDOM 21.344
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] 0.1 0.1 0.1 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.698 r_dihedral_angle_4_deg 20.371 r_dihedral_angle_3_deg 13.506 r_dihedral_angle_1_deg 7.282 r_long_range_B_refined 5.895 r_long_range_B_other 5.492 r_scangle_other 3.364 r_mcangle_other 2.545 r_mcangle_it 2.542 r_scbond_it 2.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.698 r_dihedral_angle_4_deg 20.371 r_dihedral_angle_3_deg 13.506 r_dihedral_angle_1_deg 7.282 r_long_range_B_refined 5.895 r_long_range_B_other 5.492 r_scangle_other 3.364 r_mcangle_other 2.545 r_mcangle_it 2.542 r_scbond_it 2.067 r_scbond_other 2.067 r_angle_refined_deg 1.594 r_mcbond_it 1.565 r_mcbond_other 1.557 r_angle_other_deg 0.791 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 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 4080 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing