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Crystal structure of beta-1,2-glucooligosaccharide binding protein in ligand-free form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UOR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.15M zinc acetate, 15% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.925 α = 90 b = 74.925 β = 90 c = 120.844 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 2015-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.2 50 98.8 0.097 0.047 21 5.5 38141
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 2.2 2.24 100 0.571 0.263 0.906 5.7
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 3UOR 2.2 19.24 36488 1856 99.57 0.19246 0.18975 0.1978 0.24679 0.2498 RANDOM 49.947
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] 0.23 0.12 0.23 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.729 r_dihedral_angle_4_deg 17.808 r_dihedral_angle_3_deg 16.025 r_long_range_B_refined 7.677 r_long_range_B_other 7.677 r_dihedral_angle_1_deg 6.2 r_scangle_other 5.203 r_mcangle_other 3.986 r_mcangle_it 3.985 r_scbond_it 3.435
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.729 r_dihedral_angle_4_deg 17.808 r_dihedral_angle_3_deg 16.025 r_long_range_B_refined 7.677 r_long_range_B_other 7.677 r_dihedral_angle_1_deg 6.2 r_scangle_other 5.203 r_mcangle_other 3.986 r_mcangle_it 3.985 r_scbond_it 3.435 r_scbond_other 3.434 r_mcbond_it 2.783 r_mcbond_other 2.782 r_angle_refined_deg 1.667 r_angle_other_deg 0.567 r_chiral_restr 0.088 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6093 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing MOLREP phasing PHENIX phasing