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Structure of human GGT1 in complex with ABBA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z9O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 20-25%PEG3350, 0.1M ammonium cloride, 0.1M sodium cacodilate pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.93 58.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.319 α = 90 b = 125.57 β = 90 c = 104.388 γ = 90
Symmetry Space Group C 2 2 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 PILATUS3 S 6M mirror 2017-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.0 SSRL BL14-1
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 1.42 81 98.9 0.052 25.57 4.7 128369 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.42 1.44 83.1 0.714 2.44 4.5
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 FOURIER SYNTHESIS THROUGHOUT 4Z9O 1.42 80.69 121859 6480 99.5 0.108 0.107 0.1061 0.134 0.133 RANDOM 20.71
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] -0.03 -0.17 0.2
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 44.169 r_dihedral_angle_2_deg 34.954 r_dihedral_angle_4_deg 14.373 r_sphericity_bonded 12.948 r_dihedral_angle_3_deg 12.354 r_dihedral_angle_1_deg 5.903 r_rigid_bond_restr 2.838 r_angle_refined_deg 1.654 r_angle_other_deg 1.171 r_chiral_restr 0.153
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 44.169 r_dihedral_angle_2_deg 34.954 r_dihedral_angle_4_deg 14.373 r_sphericity_bonded 12.948 r_dihedral_angle_3_deg 12.354 r_dihedral_angle_1_deg 5.903 r_rigid_bond_restr 2.838 r_angle_refined_deg 1.654 r_angle_other_deg 1.171 r_chiral_restr 0.153 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4048 Nucleic Acid Atoms Solvent Atoms 735 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing