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human CD38 in complex with nanobody MU551
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, HANGING DROP 8.5 298 0.2M sodium acetate, 0.1M Tris-HCl, 25% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.4 48.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.141 α = 90 b = 96.19 β = 90 c = 143.254 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 100 CCD ADSC QUANTUM 315r 2012-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97852 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 50 99.2 0.074 13.4 7.6 24162
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 100 0.461 7.6 2353
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 1YH3 2.2 50 22212 1200 96.35 0.1713 0.1679 0.1767 0.2366 0.2459 RANDOM 34.51
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] 0.06 0.94 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.336 r_sphericity_free 28.62 r_dihedral_angle_4_deg 16.052 r_dihedral_angle_3_deg 13.67 r_dihedral_angle_1_deg 6.191 r_sphericity_bonded 4.49 r_mcangle_it 1.374 r_angle_refined_deg 1.305 r_mcbond_it 1.071 r_mcbond_other 1.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.336 r_sphericity_free 28.62 r_dihedral_angle_4_deg 16.052 r_dihedral_angle_3_deg 13.67 r_dihedral_angle_1_deg 6.191 r_sphericity_bonded 4.49 r_mcangle_it 1.374 r_angle_refined_deg 1.305 r_mcbond_it 1.071 r_mcbond_other 1.071 r_rigid_bond_restr 0.951 r_angle_other_deg 0.918 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2958 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection