☰ Navigation Tabs
Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.85 Angstrom from unknown human gut bacteria (Uhgb_MP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VKD PDB ENTRY 1VKD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 PROTEIN WAS CRYSTALLIZED FROM 17.5% PEG 3350, 200 MM NH4CL, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.22 44.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.116 α = 90 b = 141.206 β = 90 c = 176.245 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 PIXEL MIRRORS 2014-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.8 48 98.1 0.09 10.46 4.9 190253 -1
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 1.8 1.91 88.7 0.7 1.63 3.7
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 1VKD 1.8 110.2 180598 9557 98.05 0.1571 0.15537 0.1695 0.18993 0.1985 RANDOM 34.765
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] -0.44 0.13 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.752 r_dihedral_angle_4_deg 15.614 r_dihedral_angle_3_deg 13.353 r_dihedral_angle_1_deg 6.858 r_scbond_it 2.092 r_mcangle_it 2.043 r_angle_refined_deg 1.922 r_mcbond_it 1.375 r_mcbond_other 1.375 r_angle_other_deg 0.913
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.752 r_dihedral_angle_4_deg 15.614 r_dihedral_angle_3_deg 13.353 r_dihedral_angle_1_deg 6.858 r_scbond_it 2.092 r_mcangle_it 2.043 r_angle_refined_deg 1.922 r_mcbond_it 1.375 r_mcbond_other 1.375 r_angle_other_deg 0.913 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined 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_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15371 Nucleic Acid Atoms Solvent Atoms 1063 Heterogen Atoms 312
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing