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Crystal structure of full-length mesothelin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7UED PDB entry 7UED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 289 0.9-1.1 M sodium/potassium phosphate, pH 8.2
Crystal Properties Matthews coefficient Solvent content 9.05 86.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 197.171 α = 90 b = 279.324 β = 125.091 c = 170.046 γ = 90
Symmetry Space Group C 1 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 CCD MARMOSAIC 300 mm CCD 2010-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.89197 APS 22-BM
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 3.6 50 91.4 0.123 4.87 2.5 78378
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 3.6 3.73 78.1 0.48
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 PDB entry 7UED 3.609 49.292 77988 3948 91.046 0.292 0.2908 0.244 0.3105 0.2725 128.434
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] -6.781 13.9 2.742 4.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.252 r_dihedral_angle_6_deg 9.595 r_dihedral_angle_2_deg 7.916 r_dihedral_angle_1_deg 4.687 r_lrange_it 1.93 r_lrange_other 1.93 r_mcangle_it 0.843 r_mcangle_other 0.843 r_angle_refined_deg 0.797 r_scangle_it 0.523
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.252 r_dihedral_angle_6_deg 9.595 r_dihedral_angle_2_deg 7.916 r_dihedral_angle_1_deg 4.687 r_lrange_it 1.93 r_lrange_other 1.93 r_mcangle_it 0.843 r_mcangle_other 0.843 r_angle_refined_deg 0.797 r_scangle_it 0.523 r_scangle_other 0.523 r_mcbond_it 0.457 r_mcbond_other 0.457 r_scbond_it 0.278 r_scbond_other 0.278 r_angle_other_deg 0.264 r_nbd_refined 0.191 r_symmetry_nbd_other 0.18 r_symmetry_nbd_refined 0.171 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.145 r_nbd_other 0.141 r_symmetry_nbtor_other 0.073 r_symmetry_xyhbond_nbd_refined 0.073 r_chiral_restr 0.038 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11757 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 203
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing