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Crystal structure of Fab B6-D9 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 7.2 293 7 % v/v T-mate pH 7.0, 0.1 M HEPES pH 7.2, 20 % v/v PEG Smear Medium (BCS screen, Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 3.52 65.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.045 α = 90 b = 166.045 β = 90 c = 78.769 γ = 90
Symmetry Space Group P 43 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 80 PIXEL DECTRIS EIGER2 X 16M 2022-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim 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 1.84 71.27 77 0.136 0.136 0.143 12.2 11.4 73151 34.964
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.843 2.02 68.8 1.64 12.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.84 71.27 69483 3668 76.98 0.17616 0.17443 0.20831 0.203 RANDOM 34.964
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] 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.112 r_dihedral_angle_4_deg 19.447 r_dihedral_angle_3_deg 13.889 r_dihedral_angle_1_deg 7.599 r_long_range_B_refined 6.258 r_long_range_B_other 6.09 r_scangle_other 3.782 r_mcangle_it 2.874 r_mcangle_other 2.874 r_scbond_it 2.437
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.112 r_dihedral_angle_4_deg 19.447 r_dihedral_angle_3_deg 13.889 r_dihedral_angle_1_deg 7.599 r_long_range_B_refined 6.258 r_long_range_B_other 6.09 r_scangle_other 3.782 r_mcangle_it 2.874 r_mcangle_other 2.874 r_scbond_it 2.437 r_scbond_other 2.437 r_mcbond_it 1.856 r_mcbond_other 1.851 r_angle_refined_deg 1.426 r_angle_other_deg 1.216 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5341 Nucleic Acid Atoms Solvent Atoms 696 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction XDS data reduction autoPROC data reduction autoPROC data scaling Aimless data scaling MOLREP phasing