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Crystal structure of human secretory glutaminyl cyclase in complex with PBD150
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, HANGING DROP 6.5 293 1.7M (NH4)2SO4, 4%(v/v) dioxane, 100mM Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.5 50.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.753 α = 90 b = 155.753 β = 90 c = 80.516 γ = 120
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 315r 2008-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
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 1.95 50 99.1 0.075 17.6 3.2 53608 53126 3 3
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 1.95 2.02 95.1 0.492 2.3 3.1 5382
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 2AFM 1.95 30 50358 49935 2679 99.16 0.18397 0.18107 0.2041 0.23892 0.2424 RANDOM 40.412
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] -2.47 -1.23 -2.47 3.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.845 r_dihedral_angle_4_deg 19.777 r_dihedral_angle_3_deg 17.289 r_dihedral_angle_1_deg 6.652 r_scangle_it 6.336 r_scbond_it 4.428 r_mcangle_it 2.698 r_rigid_bond_restr 2.315 r_angle_refined_deg 1.863 r_mcbond_it 1.657
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.845 r_dihedral_angle_4_deg 19.777 r_dihedral_angle_3_deg 17.289 r_dihedral_angle_1_deg 6.652 r_scangle_it 6.336 r_scbond_it 4.428 r_mcangle_it 2.698 r_rigid_bond_restr 2.315 r_angle_refined_deg 1.863 r_mcbond_it 1.657 r_chiral_restr 0.124 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 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_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5220 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 46
Software Software Software Name Purpose HKL-2000 data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing