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CRYSTAL STRUCTURE OF GID4 IN COMPLEX WITH UBF9092
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WZZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.1 M Tris-HCl 8.5, 30% PEG3350, 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.07 40.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.099 α = 90 b = 40.099 β = 90 c = 201.017 γ = 90
Symmetry Space Group P 41 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 16M 2019-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97933 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.21 50 99.5 0.053 0.057 0.018 0.998 12.2 9.8 8994
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.25 99.5 0.688 0.75 0.289 0.757 5.9
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 (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 2.21 39.36 8016 895 99.39 0.22208 0.216 0.223 0.27817 0.2816 RANDOM 57.576
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] -1.2 -1.2 2.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.109 r_dihedral_angle_3_deg 16.957 r_dihedral_angle_4_deg 10.213 r_dihedral_angle_1_deg 8.899 r_long_range_B_refined 4.886 r_long_range_B_other 4.884 r_mcangle_other 3.364 r_mcangle_it 3.359 r_scangle_other 3.333 r_mcbond_it 2.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.109 r_dihedral_angle_3_deg 16.957 r_dihedral_angle_4_deg 10.213 r_dihedral_angle_1_deg 8.899 r_long_range_B_refined 4.886 r_long_range_B_other 4.884 r_mcangle_other 3.364 r_mcangle_it 3.359 r_scangle_other 3.333 r_mcbond_it 2.279 r_scbond_it 2.268 r_mcbond_other 2.267 r_scbond_other 2.266 r_angle_refined_deg 1.448 r_angle_other_deg 1.242 r_chiral_restr 0.062 r_gen_planes_refined 0.012 r_bond_refined_d 0.01 r_gen_planes_other 0.002 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 1298 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling REFMAC phasing HKL-3000 data reduction