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DCN1 bound to inhibitor 9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 28-33% PEG 3350, 0.2 M ammonium formate
Crystal Properties Matthews coefficient Solvent content 2.02 39.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.444 α = 90 b = 85.61 β = 90 c = 125.164 γ = 90
Symmetry Space Group P 21 21 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 CCD MARMOSAIC 300 mm CCD 2018-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.7 50 100 0.081 0.089 0.034 8.7 6.7 10535 51.29
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 2.7 2.75 100 0.703 0.761 0.289 0.885 6.8
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 5V83 2.8 37.51 9324 435 99.2 0.224 0.221 0.2236 0.289 0.2997 RANDOM 42.25
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] 3.735 -3.4223 -0.3127
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.11 t_omega_torsion 2.02 t_angle_deg 0.97 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.11 t_omega_torsion 2.02 t_angle_deg 0.97 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2779 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 87
Software Software Software Name Purpose BUSTER refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing PDB_EXTRACT data extraction