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The GH130 family of mannoside phosphorylases contains glycoside hydrolases that target beta-1,2 mannosidic linkages in Candida mannan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QC2 PDB ENTRY 3QC2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 2.2 M AMMONIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 3.4 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.767 α = 90 b = 118.11 β = 90 c = 126.586 γ = 90
Symmetry Space Group P 21 2 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 2M 2014-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.35 46.58 98.3 0.05 10.7 3.4 243880 1.8 10.3
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 1.35 1.37 98.8 0.53 1.8 3.4
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3QC2 1.35 118.11 243787 12016 98.193 0.131 0.13 0.1407 0.1497 0.158 RANDOM 16.99
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] 0.802 -0.507 -0.295
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.284 r_dihedral_angle_2_deg 29.07 r_dihedral_angle_4_deg 14.452 r_sphericity_bonded 12.198 r_dihedral_angle_3_deg 11.603 r_dihedral_angle_1_deg 7.397 r_scangle_it 3.045 r_rigid_bond_restr 2.83 r_scbond_it 2.647 r_mcangle_it 2.253
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.284 r_dihedral_angle_2_deg 29.07 r_dihedral_angle_4_deg 14.452 r_sphericity_bonded 12.198 r_dihedral_angle_3_deg 11.603 r_dihedral_angle_1_deg 7.397 r_scangle_it 3.045 r_rigid_bond_restr 2.83 r_scbond_it 2.647 r_mcangle_it 2.253 r_mcbond_it 1.75 r_mcbond_other 1.731 r_angle_refined_deg 1.707 r_angle_other_deg 1.028 r_nbd_refined 0.246 r_chiral_restr 0.209 r_nbd_other 0.206 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.11 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbtor_other 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5767 Nucleic Acid Atoms Solvent Atoms 857 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing