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Crystal structure of Ixodes scapularis glutaminyl cyclase with three Cd ions bound to the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MHN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 10%(w/v) PEG8000, 8%(v/v) ethylene glycol, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.08 40.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.516 α = 90 b = 73.766 β = 90 c = 84.421 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX300HE 2017-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
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 2.36 30 98.6 0.116 10.6 4.5 13295
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 2.36 2.44 90.6 0.436 2.1 3.6
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 4MHN 2.36 25.27 12214 626 95.37 0.1866 0.1826 0.1901 0.2677 0.2661 RANDOM 34.356
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] 0.18 0.1 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.488 r_dihedral_angle_3_deg 17.015 r_dihedral_angle_4_deg 15.441 r_dihedral_angle_1_deg 7.267 r_angle_refined_deg 1.62 r_angle_other_deg 0.837 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.488 r_dihedral_angle_3_deg 17.015 r_dihedral_angle_4_deg 15.441 r_dihedral_angle_1_deg 7.267 r_angle_refined_deg 1.62 r_angle_other_deg 0.837 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2665 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing PDB_EXTRACT data extraction