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Teth514_1788 1,2-beta-oligomannan phosphorylase in complex with mannoheptaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 290 0.8M Na Citrate
0.1M Na Cacodylater pH 6.5
Crystal Properties Matthews coefficient Solvent content 6.55 81.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.11 α = 90 b = 137.11 β = 90 c = 168.638 γ = 120
Symmetry Space Group P 32 2 1
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 2019-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 50 100 0.09 0.998 6.5 7.2 81687
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 0.734 0.83
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.3 44.92 81662 4081 99.917 0.169 0.1683 0.1741 0.1751 0.1816 39.083
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] 0.177 0.089 0.177 -0.576
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.017 r_dihedral_angle_3_deg 9.745 r_dihedral_angle_1_deg 6.999 r_lrange_it 5.97 r_lrange_other 5.866 r_dihedral_angle_2_deg 4.313 r_scangle_it 3.146 r_scangle_other 3.145 r_mcangle_it 2.14 r_mcangle_other 2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.017 r_dihedral_angle_3_deg 9.745 r_dihedral_angle_1_deg 6.999 r_lrange_it 5.97 r_lrange_other 5.866 r_dihedral_angle_2_deg 4.313 r_scangle_it 3.146 r_scangle_other 3.145 r_mcangle_it 2.14 r_mcangle_other 2.14 r_scbond_it 1.78 r_scbond_other 1.78 r_mcbond_it 1.248 r_mcbond_other 1.248 r_angle_refined_deg 0.871 r_angle_other_deg 0.376 r_symmetry_nbd_other 0.21 r_nbtor_refined 0.172 r_nbd_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.14 r_symmetry_nbd_refined 0.117 r_xyhbond_nbd_refined 0.109 r_nbd_other 0.099 r_symmetry_nbtor_other 0.079 r_ncsr_local_group_1 0.046 r_chiral_restr 0.04 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4814 Nucleic Acid Atoms Solvent Atoms 515 Heterogen Atoms 179
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing