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Structure of glycosylated murine 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 5.3 294 100 mM sodium acetate, 200 mM ammonium sulfate, 12% w/v PEG2000 MME, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.43 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.24 α = 90 b = 86.87 β = 90 c = 97.16 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 165 mm 2007-04-02 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 2.9 19.753 100 0.111 10.1 4.8 8528 8528 3 56.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 100 0.508 2.4 4.1
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 (All) 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 PDB ENTRY 2AFM 2.9 19.753 8528 8527 426 99.49 0.2479 0.2479 0.2451 0.2448 0.3006 0.3179 RANDOM 48.3409
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] 2.96 -2.9 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.48 r_dihedral_angle_3_deg 25.714 r_dihedral_angle_4_deg 18.093 r_dihedral_angle_1_deg 11.331 r_scangle_it 2.729 r_angle_refined_deg 2.163 r_scbond_it 1.848 r_mcangle_it 1.373 r_mcbond_it 0.774 r_nbtor_refined 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.48 r_dihedral_angle_3_deg 25.714 r_dihedral_angle_4_deg 18.093 r_dihedral_angle_1_deg 11.331 r_scangle_it 2.729 r_angle_refined_deg 2.163 r_scbond_it 1.848 r_mcangle_it 1.373 r_mcbond_it 0.774 r_nbtor_refined 0.34 r_nbd_refined 0.335 r_xyhbond_nbd_refined 0.292 r_symmetry_vdw_refined 0.285 r_chiral_restr 0.135 r_metal_ion_refined 0.044 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2631 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 29
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling