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Crystal structure of apo-form of glutaminyl cyclase from Ixodes scapularis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AFM PDB ENTRY 2AFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 10% (w/v) PEG 8000, 8% (v/v) ethylene glycol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 41.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.388 α = 90 b = 71.146 β = 90 c = 80.121 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 ADSC QUANTUM 315 2012-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 1.0 NSRRC BL13C1
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 1.1 50 99.5 0.054 38.8 5.9 128766 128122 2 2
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 1.1 1.14 100 0.777 2.8 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 2AFM 1.1 30 122295 121598 6434 99.43 0.16561 0.16452 0.1638 0.18614 0.1855 RANDOM 16.022
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] 0.31 -0.19 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.264 r_sphericity_free 21.581 r_dihedral_angle_4_deg 12.907 r_dihedral_angle_3_deg 11.95 r_sphericity_bonded 7.85 r_dihedral_angle_1_deg 5.25 r_angle_refined_deg 1.131 r_rigid_bond_restr 0.782 r_chiral_restr 0.076 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.264 r_sphericity_free 21.581 r_dihedral_angle_4_deg 12.907 r_dihedral_angle_3_deg 11.95 r_sphericity_bonded 7.85 r_dihedral_angle_1_deg 5.25 r_angle_refined_deg 1.131 r_rigid_bond_restr 0.782 r_chiral_restr 0.076 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2665 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling