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Endo-beta-1,2-glucanase from Chitinophaga pinensis - sophorotriose and glucose complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GZH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 298 0.2 M sodium chloride, 0.1 M sodium/potassium phosphate (pH 6.2), 10% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.67 53.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.106 α = 90 b = 117.401 β = 92.56 c = 75.554 γ = 90
Symmetry Space Group C 1 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 CCD ADSC QUANTUM 210 2015-11-28 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) 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 1.7 50 99.9 0.11 13.1 3.7 120399 8.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 100 0.68 0.696 2 3.6
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 5GZH 1.7 49.46 114356 5990 99.9 0.16761 0.16598 0.1806 0.19875 0.2101 RANDOM 18.848
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.024 r_dihedral_angle_4_deg 17.516 r_dihedral_angle_3_deg 12.279 r_dihedral_angle_1_deg 6.616 r_long_range_B_refined 5.212 r_long_range_B_other 5.212 r_scangle_other 3.715 r_scbond_it 2.615 r_scbond_other 2.615 r_mcangle_it 2.369
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.024 r_dihedral_angle_4_deg 17.516 r_dihedral_angle_3_deg 12.279 r_dihedral_angle_1_deg 6.616 r_long_range_B_refined 5.212 r_long_range_B_other 5.212 r_scangle_other 3.715 r_scbond_it 2.615 r_scbond_other 2.615 r_mcangle_it 2.369 r_mcangle_other 2.369 r_angle_refined_deg 2.158 r_mcbond_it 1.846 r_mcbond_other 1.846 r_angle_other_deg 1.167 r_chiral_restr 0.147 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 6770 Nucleic Acid Atoms Solvent Atoms 666 Heterogen Atoms 141
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing