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X-ray crystal structure of CagL at pH 4.2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZCI PDB entry 3zci
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 293 30% v/v ethanol, 200 mM sodium phosphate/citric acid, pH 4.2, 5% w/v PEG 1000, 1% v/v glycerol, Microseeding
Crystal Properties Matthews coefficient Solvent content 2.69 54.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.018 α = 90 b = 63.018 β = 90 c = 243.763 γ = 120
Symmetry Space Group P 65 2 2
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 PILATUS 6M 2014-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.979450 SSRL BL11-1
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 2.3 54.58 100 0.169 19.3 37.2 13696
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 2.39 100 5.247 1.3 39.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3zci 2.3 54.58 12955 675 99.9 0.25734 0.25449 0.31283 0.2866 RANDOM 85.162
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] 2.79 1.4 2.79 -9.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.688 r_dihedral_angle_3_deg 16.298 r_dihedral_angle_4_deg 13.728 r_dihedral_angle_1_deg 5.131 r_long_range_B_refined 4.039 r_long_range_B_other 4.038 r_scangle_other 2.859 r_mcangle_it 2.326 r_mcangle_other 2.325 r_scbond_other 1.689
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.688 r_dihedral_angle_3_deg 16.298 r_dihedral_angle_4_deg 13.728 r_dihedral_angle_1_deg 5.131 r_long_range_B_refined 4.039 r_long_range_B_other 4.038 r_scangle_other 2.859 r_mcangle_it 2.326 r_mcangle_other 2.325 r_scbond_other 1.689 r_scbond_it 1.688 r_mcbond_it 1.389 r_mcbond_other 1.388 r_angle_refined_deg 1.094 r_angle_other_deg 0.846 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 1646 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection XDS data scaling Aimless data scaling Coot model building