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The Crystal Structure of UCHL1 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.1M ammonium sulfate, 2% PEG 400, 100mM HEPES, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.38 48.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.216 α = 90 b = 109.216 β = 90 c = 79.379 γ = 90
Symmetry Space Group P 4 21 2
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 9M 2022-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95374 CLSI 08ID-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 1.95 48.84 100 0.09 20.9 19.2 35583
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 1.95 2 1.056
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.95 48.84 35556 1855 99.947 0.196 0.1939 0.2018 0.2311 0.2397 40.415
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] 1.41 1.41 -2.819
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.472 r_dihedral_angle_3_deg 13.394 r_lrange_other 8.009 r_lrange_it 8.006 r_dihedral_angle_1_deg 5.914 r_scangle_other 5.855 r_scangle_it 5.85 r_dihedral_angle_2_deg 4.821 r_mcangle_it 4.342 r_mcangle_other 4.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.472 r_dihedral_angle_3_deg 13.394 r_lrange_other 8.009 r_lrange_it 8.006 r_dihedral_angle_1_deg 5.914 r_scangle_other 5.855 r_scangle_it 5.85 r_dihedral_angle_2_deg 4.821 r_mcangle_it 4.342 r_mcangle_other 4.341 r_scbond_other 3.607 r_scbond_it 3.604 r_mcbond_it 2.857 r_mcbond_other 2.856 r_angle_refined_deg 1.06 r_angle_other_deg 0.361 r_nbd_refined 0.204 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.168 r_xyhbond_nbd_refined 0.15 r_nbd_other 0.149 r_symmetry_nbd_refined 0.115 r_ncsr_local_group_1 0.096 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.054 r_symmetry_xyhbond_nbd_other 0.049 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3470 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing