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Structure of human CD38 collected by Laue diffraction
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YH3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.1 M Tris pH 8.5, 20% polyethylene glycol 10000, 8 v/v% glycerol
Crystal Properties Matthews coefficient Solvent content 2.99 58.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.704 α = 90 b = 66.6 β = 90 c = 121.8 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 300 PIXEL DECTRIS PILATUS 2M 2024-07-22 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL03HB 0.55-1.58 SSRF BL03HB
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.65 37.713 71.5 0.936 5.3 3.7 7794
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.78 0.791
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.65 37.713 7792 363 68.646 0.248 0.245 0.2471 0.3015 0.3025 40.74
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] 1.615 -1.436 -0.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.308 r_dihedral_angle_6_deg 14.723 r_dihedral_angle_2_deg 9.797 r_dihedral_angle_1_deg 7.091 r_lrange_it 6.606 r_lrange_other 6.605 r_scangle_it 4.372 r_scangle_other 4.37 r_mcangle_it 4.3 r_mcangle_other 4.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.308 r_dihedral_angle_6_deg 14.723 r_dihedral_angle_2_deg 9.797 r_dihedral_angle_1_deg 7.091 r_lrange_it 6.606 r_lrange_other 6.605 r_scangle_it 4.372 r_scangle_other 4.37 r_mcangle_it 4.3 r_mcangle_other 4.3 r_mcbond_it 2.579 r_mcbond_other 2.569 r_scbond_it 2.52 r_scbond_other 2.518 r_angle_refined_deg 1.278 r_angle_other_deg 0.473 r_symmetry_xyhbond_nbd_refined 0.426 r_nbd_other 0.279 r_nbd_refined 0.24 r_symmetry_nbd_other 0.213 r_symmetry_nbd_refined 0.196 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.164 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.064 r_symmetry_xyhbond_nbd_other 0.049 r_xyhbond_nbd_other 0.043 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1837 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Laueprocess data reduction LSCALE data scaling PHASER phasing