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Structure of ZgEngAGH5_4 in complex with a cellotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NDZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 24-24.5% PEG 3350, 160 mM MgCl2, 0.1 M Bis Tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.08 40.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.574 α = 90 b = 84.574 β = 90 c = 117.661 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 PIXEL DECTRIS PILATUS3 S 6M mirrors 2017-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97858 SOLEIL PROXIMA 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 2 45.87 99.3 0.062 0.076 0.044 0.998 12.9 2.9 63507
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 2 2.05 95.1 0.824 1.013 0.583 0.616 2.8
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 3NDZ 2.2 45.87 45421 2320 99.9 0.17659 0.17435 0.1832 0.22076 0.223 RANDOM 39.082
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] 0.93 0.46 0.93 -3.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.306 r_dihedral_angle_4_deg 16.937 r_dihedral_angle_3_deg 14.169 r_long_range_B_other 7.017 r_long_range_B_refined 7.011 r_dihedral_angle_1_deg 5.898 r_scangle_other 5.479 r_mcangle_it 4.478 r_mcangle_other 4.477 r_scbond_it 3.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.306 r_dihedral_angle_4_deg 16.937 r_dihedral_angle_3_deg 14.169 r_long_range_B_other 7.017 r_long_range_B_refined 7.011 r_dihedral_angle_1_deg 5.898 r_scangle_other 5.479 r_mcangle_it 4.478 r_mcangle_other 4.477 r_scbond_it 3.675 r_scbond_other 3.674 r_mcbond_it 3.249 r_mcbond_other 3.249 r_angle_other_deg 2.034 r_angle_refined_deg 1.495 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_bond_other_d 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 7953 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction