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CeuE (H227L, Y288F variant) a periplasmic protein from Campylobacter jejuni
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZKW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 298 0.1M MIB, pH 9.0; 25% Peg 1500.
Crystal Properties Matthews coefficient Solvent content 2.39 48.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.163 α = 82.73 b = 62.684 β = 77.33 c = 67.092 γ = 76.54
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL DECTRIS PILATUS3 6M 2016-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.98 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 60.77 96.2 0.085 0.995 7.4 3.5 78620
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 96.4 0.983 0.459 1.2 3.4
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 3ZKW 1.8 60.77 74635 3985 96.2 0.19708 0.19473 0.2024 0.23981 0.2447 RANDOM 34.981
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] -0.38 -2.13 0.6 0.6 1.09 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.109 r_dihedral_angle_4_deg 15.883 r_dihedral_angle_3_deg 15.695 r_long_range_B_other 6.874 r_long_range_B_refined 6.871 r_dihedral_angle_1_deg 6.52 r_scangle_other 5.671 r_mcangle_it 4.264 r_mcangle_other 4.264 r_scbond_it 3.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.109 r_dihedral_angle_4_deg 15.883 r_dihedral_angle_3_deg 15.695 r_long_range_B_other 6.874 r_long_range_B_refined 6.871 r_dihedral_angle_1_deg 6.52 r_scangle_other 5.671 r_mcangle_it 4.264 r_mcangle_other 4.264 r_scbond_it 3.874 r_scbond_other 3.874 r_mcbond_it 3.182 r_mcbond_other 3.18 r_angle_refined_deg 1.864 r_angle_other_deg 1.083 r_chiral_restr 0.117 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 6342 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing xia2 data scaling