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Crystal Structure of Cadherin8 EC1 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZVN PDB entry 1ZVN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 22% PEG 4000, 0.1M HEPES pH7, 0.1M NaAcetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.69 53.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.196 α = 90 b = 39.934 β = 110.68 c = 66.439 γ = 90
Symmetry Space Group P 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 110 CCD MARRESEARCH mirrors 2003-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9792 APS 31-ID
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 1.99 30 99 0.078 10.4 2.8 15376 15229 -3
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 1.99 2.06 97.3 0.201 3.9 2.7 1469
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1ZVN 2 20 14686 14686 776 99.34 0.25358 0.25358 0.25201 0.28336 RANDOM 10.412
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] 1.68 1.65 -2.9 2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.254 r_dihedral_angle_4_deg 19.749 r_dihedral_angle_3_deg 15.239 r_dihedral_angle_1_deg 6.373 r_scangle_it 2.518 r_scbond_it 1.589 r_angle_refined_deg 1.439 r_mcangle_it 1.043 r_mcbond_it 0.75 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.254 r_dihedral_angle_4_deg 19.749 r_dihedral_angle_3_deg 15.239 r_dihedral_angle_1_deg 6.373 r_scangle_it 2.518 r_scbond_it 1.589 r_angle_refined_deg 1.439 r_mcangle_it 1.043 r_mcbond_it 0.75 r_nbtor_refined 0.311 r_nbd_refined 0.235 r_symmetry_vdw_refined 0.2 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 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_refined 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 1519 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing