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Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with HEPES
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZDC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 292 1 M sodium succinate pH 7.0, 1% w/v PEG-MME2000
Protein at 10 mg/ml in buffer: 25 mM HEPES pH 7.0, 200 mM NaCl
100 nl protein solution and 200 nl reservoir solution.
Crystal Properties Matthews coefficient Solvent content 2.71 54.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.245 α = 90 b = 144.245 β = 90 c = 139.661 γ = 90
Symmetry Space Group P 43 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 2017-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3 102.205 100 0.582 0.611 0.135 0.974 5 20.3 30161 41.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.16 99.8 1.175 1.205 0.265 0.253 2.9 20.5
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 (All) 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 6ZDC 3 102.205 30099 1429 99.947 0.218 0.2153 0.2153 0.2687 0.2687 RANDOM 49.027
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] 0.31 0.31 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.265 r_dihedral_angle_3_deg 19.232 r_dihedral_angle_4_deg 17.66 r_lrange_it 7.502 r_dihedral_angle_1_deg 5.968 r_scangle_it 4.687 r_mcangle_it 4.566 r_scbond_it 2.899 r_mcbond_it 2.769 r_angle_refined_deg 1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.265 r_dihedral_angle_3_deg 19.232 r_dihedral_angle_4_deg 17.66 r_lrange_it 7.502 r_dihedral_angle_1_deg 5.968 r_scangle_it 4.687 r_mcangle_it 4.566 r_scbond_it 2.899 r_mcbond_it 2.769 r_angle_refined_deg 1.7 r_nbtor_refined 0.298 r_symmetry_xyhbond_nbd_refined 0.249 r_symmetry_nbd_refined 0.205 r_nbd_refined 0.18 r_chiral_restr 0.126 r_xyhbond_nbd_refined 0.11 r_ncsr_local_group_2 0.085 r_ncsr_local_group_1 0.082 r_ncsr_local_group_3 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8853 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing