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ZHD complex with hydrolyzed alpha-ZOL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 ammonium phosphate, imidazole, potassium chloride
Crystal Properties Matthews coefficient Solvent content 3.05 59.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.575 α = 90 b = 89.887 β = 90 c = 112.996 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 EIGER X 16M 2017-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97776 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.65 40 100 0.073 0.02 0.984 37.9 13.3 91757
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 0.666 0.18 0.939
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5c8z 1.65 35 87021 4651 99.75 0.14084 0.13995 0.1571 0.1672 RANDOM 18.765
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] -0.74 0.69 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.362 r_dihedral_angle_4_deg 12.478 r_dihedral_angle_3_deg 11.388 r_dihedral_angle_1_deg 6.409 r_long_range_B_refined 5.529 r_long_range_B_other 5.455 r_scangle_other 4.787 r_scbond_it 3.333 r_scbond_other 3.332 r_mcangle_it 2.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.362 r_dihedral_angle_4_deg 12.478 r_dihedral_angle_3_deg 11.388 r_dihedral_angle_1_deg 6.409 r_long_range_B_refined 5.529 r_long_range_B_other 5.455 r_scangle_other 4.787 r_scbond_it 3.333 r_scbond_other 3.332 r_mcangle_it 2.306 r_mcangle_other 2.306 r_angle_refined_deg 1.882 r_mcbond_it 1.706 r_mcbond_other 1.702 r_angle_other_deg 1.664 r_chiral_restr 0.115 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 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 4110 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing