☰ Navigation Tabs
Structure of glycosylated human glutaminyl cyclase
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, HANGING DROP 8 294 100 mM imidazole, 30% v/v MPD, 11% w/v PEG4000, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.57 52.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.408 α = 90 b = 63.688 β = 105.76 c = 77.159 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 CCD RAYONIX MX-225 2009-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.1 11.981 96 0.089 7.1 3 21435 21435 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 96.3 0.409 0.409 1.9 2.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2AFM 2.1 11.98 21435 20342 1073 95.36 0.20681 0.20382 0.26358 0.2914 RANDOM 36.952
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] -1.02 2.05 -3.81 5.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.838 r_dihedral_angle_4_deg 22.096 r_dihedral_angle_3_deg 17.344 r_dihedral_angle_1_deg 7.344 r_scangle_it 3.805 r_scbond_it 2.603 r_angle_refined_deg 1.996 r_mcangle_it 1.54 r_mcbond_it 0.971 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.838 r_dihedral_angle_4_deg 22.096 r_dihedral_angle_3_deg 17.344 r_dihedral_angle_1_deg 7.344 r_scangle_it 3.805 r_scbond_it 2.603 r_angle_refined_deg 1.996 r_mcangle_it 1.54 r_mcbond_it 0.971 r_chiral_restr 0.129 r_bond_refined_d 0.023 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2536 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 35
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection XSCALE data scaling