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Plant N-glycan specific alpha-1,3-mannosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WVX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 200 mM Potassium citrate and 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.32 46.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.941 α = 90 b = 84.335 β = 90 c = 132.581 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 PIXEL DECTRIS PILATUS 6M 2017-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 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 1.43 66.29 98.8 0.082 0.095 0.048 0.998 9.7 7.1 135130
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 1.43 1.45 1.196 1.444 0.794 0.502 5.9
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2wvx 1.43 66.29 134810 6731 98.519 0.135 0.1327 0.1725 0.1663 18.793
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] 0.932 -0.799 -0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.638 r_dihedral_angle_6_deg 17.198 r_dihedral_angle_3_deg 12.849 r_dihedral_angle_other_3_deg 7.213 r_dihedral_angle_1_deg 6.662 r_lrange_it 3.862 r_lrange_other 3.572 r_scangle_it 3.213 r_scangle_other 3.213 r_scbond_it 2.721
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.638 r_dihedral_angle_6_deg 17.198 r_dihedral_angle_3_deg 12.849 r_dihedral_angle_other_3_deg 7.213 r_dihedral_angle_1_deg 6.662 r_lrange_it 3.862 r_lrange_other 3.572 r_scangle_it 3.213 r_scangle_other 3.213 r_scbond_it 2.721 r_scbond_other 2.7 r_mcangle_it 2.398 r_mcangle_other 2.398 r_rigid_bond_restr 2.162 r_mcbond_it 1.954 r_mcbond_other 1.947 r_angle_refined_deg 1.225 r_angle_other_deg 0.444 r_metal_ion_refined 0.28 r_symmetry_nbd_refined 0.256 r_nbd_other 0.234 r_nbd_refined 0.224 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.143 r_xyhbond_nbd_refined 0.129 r_symmetry_xyhbond_nbd_other 0.128 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.065 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5591 Nucleic Acid Atoms Solvent Atoms 646 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement Coot model building MolProbity model building PHASER phasing pointless data scaling xia2 data reduction XDS data reduction