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Crystal Structure of double mutant Y115E Y117E human Glutaminyl Cyclase in complex with inhibitor PBD-150
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 281 0.1 M MES buffer pH 6.5, 1.6 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.52 51.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.429 α = 90 b = 149.54 β = 96.82 c = 96.21 γ = 90
Symmetry Space Group C 1 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 100 PIXEL DECTRIS PILATUS 2M 2014-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.979 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 32.99 99 6 2.9 257040 87147
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 2AFM 1.95 32.99 82798 4184 98.77 0.1663 0.16408 0.1754 0.21101 0.2199 RANDOM 13.098
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.305 r_dihedral_angle_4_deg 19.288 r_dihedral_angle_3_deg 12.446 r_dihedral_angle_1_deg 6.675 r_long_range_B_refined 6.006 r_long_range_B_other 5.613 r_scangle_other 2.804 r_mcangle_it 2.247 r_mcangle_other 2.247 r_angle_refined_deg 1.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.305 r_dihedral_angle_4_deg 19.288 r_dihedral_angle_3_deg 12.446 r_dihedral_angle_1_deg 6.675 r_long_range_B_refined 6.006 r_long_range_B_other 5.613 r_scangle_other 2.804 r_mcangle_it 2.247 r_mcangle_other 2.247 r_angle_refined_deg 1.912 r_scbond_it 1.784 r_scbond_other 1.771 r_mcbond_it 1.342 r_mcbond_other 1.342 r_angle_other_deg 0.984 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.003 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 7752 Nucleic Acid Atoms Solvent Atoms 1301 Heterogen Atoms 175
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing