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Crystal structure of human CD38 ECD in complex with UniDab(TM) F11A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YH3 1YH3, 6PZW experimental model PDB 6PZW 1YH3, 6PZW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Sodium Citrate, PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.91 57.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.82 α = 90 b = 64.82 β = 90 c = 201.316 γ = 120
Symmetry Space Group P 32 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 100 PIXEL DECTRIS EIGER X 16M 2020-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 1.79 49.08 100 0.083 0.999 12.1 10.1 47342
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 1.79 1.83 1.379 0.653
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1YH3, 6PZW 1.9 49.075 39716 1962 99.987 0.195 0.1927 0.2018 0.2308 0.2395 37.307
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] 0.102 0.051 0.102 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.475 r_dihedral_angle_4_deg 18.977 r_dihedral_angle_3_deg 15.041 r_lrange_it 8.512 r_lrange_other 8.409 r_dihedral_angle_1_deg 6.898 r_scangle_it 6.052 r_scangle_other 6.05 r_mcangle_it 4.764 r_mcangle_other 4.763
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.475 r_dihedral_angle_4_deg 18.977 r_dihedral_angle_3_deg 15.041 r_lrange_it 8.512 r_lrange_other 8.409 r_dihedral_angle_1_deg 6.898 r_scangle_it 6.052 r_scangle_other 6.05 r_mcangle_it 4.764 r_mcangle_other 4.763 r_scbond_it 4.029 r_scbond_other 4.027 r_mcbond_other 3.208 r_mcbond_it 3.207 r_angle_other_deg 2.381 r_angle_refined_deg 1.6 r_symmetry_nbd_other 0.231 r_nbd_other 0.223 r_nbd_refined 0.22 r_symmetry_xyhbond_nbd_refined 0.214 r_symmetry_nbd_refined 0.212 r_xyhbond_nbd_refined 0.193 r_nbtor_refined 0.164 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.074 r_symmetry_xyhbond_nbd_other 0.057 r_bond_other_d 0.035 r_xyhbond_nbd_other 0.024 r_bond_refined_d 0.01 r_gen_planes_other 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3003 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing