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Crystal Structure of AtlA catalytic domain from Enterococcus feacalis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FI7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Magnesium chloride, 10% polyethylene glycol (PEG) 3000 and 0.1M Na-Cacodylate pH 6.5.
Crystal Properties Matthews coefficient Solvent content 2.67 53.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.549 α = 90 b = 62.549 β = 90 c = 93.219 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 120 PIXEL DECTRIS PILATUS 6M 2018-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9762 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.45 54 99.89 0.99 9.8 4.7 38042
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.47 0.76
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 3FI7 1.45 46.88 36010 1991 99.89 0.1326 0.1306 0.1322 0.1677 0.1391 RANDOM 26.072
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] -0.37 -0.19 -0.37 1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.741 r_sphericity_free 31.903 r_sphericity_bonded 20.493 r_dihedral_angle_4_deg 12.851 r_dihedral_angle_3_deg 12.354 r_dihedral_angle_1_deg 5.865 r_rigid_bond_restr 3.697 r_angle_refined_deg 1.861 r_angle_other_deg 1.169 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.741 r_sphericity_free 31.903 r_sphericity_bonded 20.493 r_dihedral_angle_4_deg 12.851 r_dihedral_angle_3_deg 12.354 r_dihedral_angle_1_deg 5.865 r_rigid_bond_restr 3.697 r_angle_refined_deg 1.861 r_angle_other_deg 1.169 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1281 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction MOLREP phasing PDB_EXTRACT data extraction SCALA data scaling