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CD44 PanDDA analysis group deposition -- The hyaluronan-binding domain of CD44 in complex with Z2856434878
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JCP 2JCP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 200mM ammonium sulphate, 100mM MES, 24% PEG 5,000 MME
Crystal Properties Matthews coefficient Solvent content 2.08 40.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.735 α = 90 b = 81.362 β = 117.95 c = 31.989 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2021-03-06 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91199 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.27 40.68 96.5 0.134 0.157 0.081 0.993 5.3 3.5 34946 12.09
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.27 1.34 94.2 1.496 1.801 0.987 0.443 3 5002
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2JCP 1.274 40.68 34770 1748 95.9 0.1901 0.1879 0.2337 0.2304 RANDOM 16.22
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] 1.6207 -0.198 -4.6856 3.0649
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.04 t_omega_torsion 5.43 t_angle_deg 1.15 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.04 t_omega_torsion 5.43 t_angle_deg 1.15 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1171 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 41
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing