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Crystal structure of cadherin-6 EC12 W4A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 293 0.1M HEPES pH 7.5, 17% (v/v) isopropanol, 12% (w/v) PEG 4000, 9mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 47.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.979 α = 90 b = 113.555 β = 96.01 c = 67.907 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 CCD ADSC QUANTUM 4 2008-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A NSLS X4A
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 2.82 50 98.4 0.088 12.9 3.3 20165 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2.82 20 20529 19102 1021 98.9 0.211 0.207 0.2094 0.282 0.2784 RANDOM 58.62
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] 4.27 1.08 -2.51 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.677 r_dihedral_angle_4_deg 19.36 r_dihedral_angle_3_deg 17.546 r_dihedral_angle_1_deg 5.921 r_angle_refined_deg 1.051 r_scangle_it 0.785 r_scbond_it 0.489 r_mcangle_it 0.401 r_nbtor_refined 0.3 r_mcbond_it 0.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.677 r_dihedral_angle_4_deg 19.36 r_dihedral_angle_3_deg 17.546 r_dihedral_angle_1_deg 5.921 r_angle_refined_deg 1.051 r_scangle_it 0.785 r_scbond_it 0.489 r_mcangle_it 0.401 r_nbtor_refined 0.3 r_mcbond_it 0.227 r_symmetry_hbond_refined 0.196 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.133 r_metal_ion_refined 0.118 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6229 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 12
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling