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Crystal structure of Fab E2-RecA in complex with CD38
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DUN experimental model PDB 7DHA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 70% v/v MPD, 0.1M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.01 59.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.29 α = 90 b = 61.07 β = 108.6 c = 124.12 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER2 X 16M 2022-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9998 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.7 47.22 99.85 0.307 0.99 6.62 7 24595
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 99.64 2.88 3.32 0.44 0.72
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 2.7 47.22 24595 1295 99.85 0.24481 0.24304 0.2478 0.27926 0.2838 RANDOM 82.112
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] 1.71 4.22 -3.97 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.545 r_dihedral_angle_1_deg 5.326 r_long_range_B_refined 2.729 r_long_range_B_other 2.682 r_dihedral_angle_2_deg 1.761 r_mcangle_it 1.439 r_mcangle_other 1.438 r_scangle_other 1.194 r_mcbond_it 0.821 r_mcbond_other 0.821
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.545 r_dihedral_angle_1_deg 5.326 r_long_range_B_refined 2.729 r_long_range_B_other 2.682 r_dihedral_angle_2_deg 1.761 r_mcangle_it 1.439 r_mcangle_other 1.438 r_scangle_other 1.194 r_mcbond_it 0.821 r_mcbond_other 0.821 r_scbond_it 0.669 r_scbond_other 0.669 r_angle_refined_deg 0.61 r_angle_other_deg 0.247 r_chiral_restr 0.03 r_bond_refined_d 0.002 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 5309 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing