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E1 enzyme for ubiquitin like protein activation in complex with UBL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H78
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 293.15 0.2 M Lithium Nitrate, 21% PEG 3350, 0.2 M Magnesium chloride hexahydrate and 3.5 % v/v Pentaerythritol ethoxylate (3/4 EO/OH)
Crystal Properties Matthews coefficient Solvent content 2.46 49.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.11 α = 90 b = 105.52 β = 102.29 c = 93.88 γ = 90
Symmetry Space Group P 1 21 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 2017-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9762 ESRF ID29
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 2.1 58.53 98.5 0.112 0.995 5.8 3.8 92451
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 2.1 2.14 1.814 0.517 0.8
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 6H78 2.1 52.76 92451 2369 98 0.18492 0.18401 0.184 0.22089 0.2222 RANDOM 54.119
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] -2.55 0.2 6.49 -3.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.191 r_dihedral_angle_4_deg 19.999 r_dihedral_angle_3_deg 18.042 r_long_range_B_refined 14.069 r_scbond_it 11.566 r_mcangle_it 9.055 r_mcbond_it 7.849 r_dihedral_angle_1_deg 5.565 r_angle_refined_deg 1.498 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.191 r_dihedral_angle_4_deg 19.999 r_dihedral_angle_3_deg 18.042 r_long_range_B_refined 14.069 r_scbond_it 11.566 r_mcangle_it 9.055 r_mcbond_it 7.849 r_dihedral_angle_1_deg 5.565 r_angle_refined_deg 1.498 r_chiral_restr 0.11 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11700 Nucleic Acid Atoms Solvent Atoms 515 Heterogen Atoms 297
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing