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Horcolin complex with methyl-alpha-mannose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X1V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 298 0.2 M Magnesium chloride hexahydrate,
0.1 M TRIS hydrochloride pH 8.5,
30% w/v Polyethylene glycol 4,000
Crystal Properties Matthews coefficient Solvent content 2.46 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.84 α = 90 b = 42.84 β = 90 c = 139.201 γ = 120
Symmetry Space Group P 31 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 PILATUS3 6M 2019-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.2 46.4 97.3 0.128 0.038 0.99 10.5 12 45978 11.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.26 95 0.98 0.289 0.77 2.3 12
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1X1V 1.2 37.128 45952 2326 96.761 0.211 0.2094 0.2094 0.2346 0.2342 13.729
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] 0.169 0.084 0.169 -0.547
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.684 r_dihedral_angle_4_deg 24.444 r_dihedral_angle_3_deg 11.672 r_dihedral_angle_1_deg 6.754 r_lrange_it 5.188 r_lrange_other 4.455 r_scangle_it 3.259 r_scangle_other 3.257 r_angle_other_deg 2.436 r_scbond_it 2.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.684 r_dihedral_angle_4_deg 24.444 r_dihedral_angle_3_deg 11.672 r_dihedral_angle_1_deg 6.754 r_lrange_it 5.188 r_lrange_other 4.455 r_scangle_it 3.259 r_scangle_other 3.257 r_angle_other_deg 2.436 r_scbond_it 2.153 r_scbond_other 2.151 r_mcangle_other 2.009 r_mcangle_it 2.008 r_angle_refined_deg 1.981 r_mcbond_it 1.316 r_mcbond_other 1.301 r_symmetry_nbd_other 0.21 r_symmetry_xyhbond_nbd_refined 0.203 r_nbd_other 0.176 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.166 r_nbd_refined 0.151 r_symmetry_nbtor_other 0.111 r_symmetry_nbd_refined 0.095 r_chiral_restr 0.092 r_bond_other_d 0.036 r_bond_refined_d 0.016 r_gen_planes_other 0.015 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1039 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing