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DPP9 bound to a dipeptide (MP) from the N-terminus of BRCA2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EOQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.25 293 20 mg/ml of protein, 10% PEG 8000, 25% glycerol, 0.16 M calcium acetate, 0.08 M cacodilate pH 6.25. Drops are set in a 1:1 ratio.
Crystal Properties Matthews coefficient Solvent content 2.68 54.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.516 α = 90 b = 117.219 β = 105.72 c = 163.401 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-F 2018-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00002 SLS X10SA
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 3 43.47 87.8 0.13 0.98 5.9 2.65 76534
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 3 3.19 88.8 0.3 0.93 3
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 6EOQ 3 43.47 72706 3827 88.08 0.28871 0.28573 0.2872 0.34517 0.3445 RANDOM 25.557
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] -2.81 -0.23 3.79 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.113 r_dihedral_angle_3_deg 18.554 r_dihedral_angle_4_deg 18.169 r_dihedral_angle_1_deg 7.218 r_long_range_B_refined 3.67 r_long_range_B_other 3.67 r_mcangle_it 2.036 r_mcangle_other 2.036 r_scangle_other 1.526 r_mcbond_it 1.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.113 r_dihedral_angle_3_deg 18.554 r_dihedral_angle_4_deg 18.169 r_dihedral_angle_1_deg 7.218 r_long_range_B_refined 3.67 r_long_range_B_other 3.67 r_mcangle_it 2.036 r_mcangle_other 2.036 r_scangle_other 1.526 r_mcbond_it 1.136 r_mcbond_other 1.136 r_angle_refined_deg 1.12 r_scbond_it 0.839 r_scbond_other 0.838 r_angle_other_deg 0.348 r_chiral_restr 0.046 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26312 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing