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Glycoside hydrolase-like protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ACY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 293 100 mM Tris pH 8.0
20 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.72 54.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.054 α = 90 b = 102.054 β = 90 c = 80.113 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 100 PIXEL DECTRIS PILATUS 6M 2016-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 88.38 100 0.112 0.998 13.6 9.6 19223
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 100 0.741 0.783 0.25 0.86 3 9.8
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 4acy 2.4 88.38 18190 1011 99.95 0.16644 0.16386 0.1688 0.21468 0.2206 RANDOM 47.336
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] 1.01 0.51 1.01 -3.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.156 r_dihedral_angle_3_deg 14.846 r_dihedral_angle_4_deg 14.481 r_long_range_B_other 6.866 r_long_range_B_refined 6.865 r_dihedral_angle_1_deg 6.489 r_scangle_other 5.607 r_mcangle_it 4.848 r_mcangle_other 4.847 r_scbond_it 3.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.156 r_dihedral_angle_3_deg 14.846 r_dihedral_angle_4_deg 14.481 r_long_range_B_other 6.866 r_long_range_B_refined 6.865 r_dihedral_angle_1_deg 6.489 r_scangle_other 5.607 r_mcangle_it 4.848 r_mcangle_other 4.847 r_scbond_it 3.959 r_scbond_other 3.958 r_mcbond_it 3.4 r_mcbond_other 3.393 r_angle_refined_deg 1.653 r_angle_other_deg 0.996 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 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 2846 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing