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Crystal structure of the mutant W207F of human secretory glutaminyl cyclase
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 3 59.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.754 α = 90 b = 118.754 β = 90 c = 332.093 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 99.7 0.047 40.3 5.3 66061 65863 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 99.8 0.491 3.1 5.4 6529
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 62654 62497 3335 99.75 0.14504 0.14264 0.1724 0.1904 0.1674 RANDOM 36.352
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 0.09 0.18 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.94 r_dihedral_angle_4_deg 17.615 r_dihedral_angle_3_deg 13.677 r_scangle_it 7.352 r_dihedral_angle_1_deg 6.382 r_scbond_it 5.051 r_mcangle_it 3.193 r_rigid_bond_restr 2.919 r_mcbond_it 2.095 r_angle_refined_deg 1.903
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.94 r_dihedral_angle_4_deg 17.615 r_dihedral_angle_3_deg 13.677 r_scangle_it 7.352 r_dihedral_angle_1_deg 6.382 r_scbond_it 5.051 r_mcangle_it 3.193 r_rigid_bond_restr 2.919 r_mcbond_it 2.095 r_angle_refined_deg 1.903 r_chiral_restr 0.164 r_bond_refined_d 0.029 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 5214 Nucleic Acid Atoms Solvent Atoms 507 Heterogen Atoms 12
Software Software Software Name Purpose HKL-2000 data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing