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Structure of C113A/C136A mutant variant of glycosylated glutaminyl cyclase from Drosophila melanogaster
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F9U PDB ENTRY 4F9U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 12% PEG8000, 2 mM PQ50, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.42 64.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.865 α = 90 b = 170.865 β = 90 c = 57.236 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 RAYONIX MX-225 mirrors 2010-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 2.1 147.973 98 0.113 9.4 3.8 55222 55179 -3.7 27
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 2.1 2.21 99 0.678 1.9 3.8 8055
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 4F9U 2.1 50 55222 55179 2807 98.45 0.176 0.176 0.174 0.1776 0.215 0.1835 RANDOM 21.132
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] -0.67 -0.34 -0.67 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.515 r_dihedral_angle_4_deg 18.888 r_dihedral_angle_3_deg 13.158 r_dihedral_angle_1_deg 5.809 r_scangle_it 3.311 r_scbond_it 2.08 r_angle_refined_deg 1.414 r_mcangle_it 1.34 r_angle_other_deg 0.901 r_mcbond_it 0.726
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.515 r_dihedral_angle_4_deg 18.888 r_dihedral_angle_3_deg 13.158 r_dihedral_angle_1_deg 5.809 r_scangle_it 3.311 r_scbond_it 2.08 r_angle_refined_deg 1.414 r_mcangle_it 1.34 r_angle_other_deg 0.901 r_mcbond_it 0.726 r_mcbond_other 0.163 r_chiral_restr 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4854 Nucleic Acid Atoms Solvent Atoms 685 Heterogen Atoms 175
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling