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Murine endoplasmic reticulum alpha-glucosidase II with N-9'-methoxynonyl-1-deoxynojirimycin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F0E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 21% v/v ethylene glycol, 11% w/v PEG 8000 (from the Morpheus Precipitant Mix 2), 50 mM Morpheus carboxylic acids mix, 100 mM Morpheus buffer system 1 pH 6.25
Crystal Properties Matthews coefficient Solvent content 2.65 53.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.321 α = 90 b = 173.311 β = 90 c = 63.032 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2016-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 1.07205 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 1.822 104.321 100 0.129 0.998 12.1 6.7 102902 24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.822 1.828 97.5 2.1 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS THROUGHOUT 5F0E 1.822 89.38 102823 5057 99.7 0.176 0.175 0.1781 0.195 0.197 RANDOM 26.13
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] 1.1577 0.0282 -1.1858
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.16 t_omega_torsion 4.25 t_angle_deg 1.01 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.16 t_omega_torsion 4.25 t_angle_deg 1.01 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7562 Nucleic Acid Atoms Solvent Atoms 490 Heterogen Atoms 163
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction Aimless data scaling BUSTER phasing