☰ Navigation Tabs
Structure and function of a novel periplasmic chitooligosaccharide-binding protein from marine Vibrio bacteria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZU0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 0.09M Halogens (NaF, NaBr, NaI), 0.1M Buffer 2 (HEPES/MOPS) pH 7.5, 37.5% MPD_P1K_P3350 mix
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.73 α = 90 b = 54.73 β = 90 c = 306.442 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 95 PIXEL DECTRIS PILATUS 6M-F Fixed monochromator 2017-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.36 46.8 99.8 0.132 0.139 0.044 0.995 7.6 9.5 115984
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.4 97.7 1.659 1.807 0.948 0.067 1.2 6.8
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 1ZU0 1.36 46.84 107022 5473 96.67 0.19666 0.19514 0.1952 0.22622 0.2262 RANDOM 17.552
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] 0.27 0.13 0.27 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.823 r_dihedral_angle_4_deg 16.967 r_dihedral_angle_3_deg 13.533 r_dihedral_angle_1_deg 6.673 r_long_range_B_refined 5.376 r_scbond_it 2.935 r_mcangle_it 2.226 r_angle_refined_deg 2.209 r_mcbond_it 1.599 r_chiral_restr 0.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.823 r_dihedral_angle_4_deg 16.967 r_dihedral_angle_3_deg 13.533 r_dihedral_angle_1_deg 6.673 r_long_range_B_refined 5.376 r_scbond_it 2.935 r_mcangle_it 2.226 r_angle_refined_deg 2.209 r_mcbond_it 1.599 r_chiral_restr 0.185 r_bond_refined_d 0.03 r_gen_planes_refined 0.016 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 4260 Nucleic Acid Atoms Solvent Atoms 461 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing