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Crystal structure and binding properties of the CD2 and CD244 (2B4) binding protein, CD48
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CCZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M sodium HEPES, 1.5M lithium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.5 64.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.78 α = 90 b = 96.78 β = 90 c = 126.61 γ = 90
Symmetry Space Group I 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 1999-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID2 0.977 ESRF ID2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 30 98.5 9426 2 2 49.5
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 1CCZ 2.6 24.2 9400 501 98.2 0.214 0.214 0.2206 0.271 0.2777 RANDOM 58.7
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] 7.19 7.19 -14.37
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.7 c_scangle_it 6.94 c_scbond_it 4.9 c_mcangle_it 4.33 c_mcbond_it 2.66 c_angle_deg 1.6 c_improper_angle_d 0.88 c_bond_d 0.01 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.7 c_scangle_it 6.94 c_scbond_it 4.9 c_mcangle_it 4.33 c_mcbond_it 2.66 c_angle_deg 1.6 c_improper_angle_d 0.88 c_bond_d 0.01 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1481 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 72
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing