☰ Navigation Tabs
Teth514_1788 1,2-beta-oligomannan phosphorylase in complex with mannose (+1) and phosphate
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, SITTING DROP 285 0.1 M Sodium cacodylate trihydrate pH 6.5, 1.0 M Sodium citrate tribasic dihydrate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.269 α = 90 b = 137.269 β = 90 c = 169.384 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 2018-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9677 ESRF MASSIF-1
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 2.5 50 99.8 0.112 0.996 6.4 5.7 64153
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 0.757
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 2.5 44.972 64104 3113 99.763 0.152 0.1505 0.1609 0.1721 0.1783 34.922
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] 0.017 0.009 0.017 -0.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.476 r_dihedral_angle_3_deg 12.966 r_lrange_it 8.231 r_lrange_other 8.23 r_dihedral_angle_1_deg 7.517 r_scangle_it 6.445 r_scangle_other 6.444 r_dihedral_angle_2_deg 5.76 r_scbond_it 3.904 r_scbond_other 3.903
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.476 r_dihedral_angle_3_deg 12.966 r_lrange_it 8.231 r_lrange_other 8.23 r_dihedral_angle_1_deg 7.517 r_scangle_it 6.445 r_scangle_other 6.444 r_dihedral_angle_2_deg 5.76 r_scbond_it 3.904 r_scbond_other 3.903 r_mcangle_it 3.093 r_mcangle_other 3.093 r_mcbond_it 2 r_mcbond_other 2 r_angle_refined_deg 1.293 r_angle_other_deg 0.468 r_symmetry_nbd_other 0.194 r_nbd_refined 0.181 r_nbd_other 0.179 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.146 r_symmetry_xyhbond_nbd_refined 0.13 r_symmetry_nbd_refined 0.123 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.062 r_ncsr_local_group_1 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4807 Nucleic Acid Atoms Solvent Atoms 652 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing