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Crystal structure of human glutaminyl cyclase variant Y115E-Y117E in complex with SEN177
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YU9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277.15 0.1 M MES, 0.4 M ammonium sulfate, 0.07 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.44 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.14 α = 90 b = 149.81 β = 97.18 c = 95.98 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 2013-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9795 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.72 95.23 99.8 0.13 0.985 5.3 3.4 126884 9.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.75 99.4 0.75 0.567 1.7 2.9
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 4yu9 1.72 95.23 120334 6549 99.81 0.15948 0.15819 0.169 0.18307 0.1941 RANDOM 15.516
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 30.74 r_dihedral_angle_4_deg 19.976 r_dihedral_angle_3_deg 11.677 r_dihedral_angle_1_deg 6.631 r_long_range_B_refined 4.938 r_long_range_B_other 4.935 r_scangle_other 3.741 r_mcangle_it 2.703 r_mcangle_other 2.703 r_scbond_it 2.419
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.74 r_dihedral_angle_4_deg 19.976 r_dihedral_angle_3_deg 11.677 r_dihedral_angle_1_deg 6.631 r_long_range_B_refined 4.938 r_long_range_B_other 4.935 r_scangle_other 3.741 r_mcangle_it 2.703 r_mcangle_other 2.703 r_scbond_it 2.419 r_scbond_other 2.418 r_mcbond_it 1.632 r_mcbond_other 1.631 r_angle_refined_deg 1.617 r_angle_other_deg 0.623 r_chiral_restr 0.15 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 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 7841 Nucleic Acid Atoms Solvent Atoms 697 Heterogen Atoms 173
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing