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Crystal structure of chicken T-cadherin EC1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K6F PDB entry 3K6F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 50mM Zn acetate, 20 % PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.6 52.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.153 α = 90 b = 44.93 β = 90 c = 56.666 γ = 90
Symmetry Space Group P 21 21 21
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 315 Horizontal focusing sagitally bent second mono crystal M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9791 NSLS X29A
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 1.1 20 99.8 0.117 11.7 5.7 42837
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 1.15 97.3 0.186 6.4
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 PDB entry 3K6F 1.13 18.7 42834 2176 99.88 0.143 0.142 0.1506 0.158 0.1548 RANDOM 13.631
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] -0.29 0.1 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.459 r_dihedral_angle_1_deg 15.012 r_dihedral_angle_4_deg 14.509 r_dihedral_angle_3_deg 11.593 r_sphericity_free 4.594 r_scangle_it 4.101 r_sphericity_bonded 3.862 r_scbond_it 2.806 r_mcangle_it 2.271 r_angle_refined_deg 2.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.459 r_dihedral_angle_1_deg 15.012 r_dihedral_angle_4_deg 14.509 r_dihedral_angle_3_deg 11.593 r_sphericity_free 4.594 r_scangle_it 4.101 r_sphericity_bonded 3.862 r_scbond_it 2.806 r_mcangle_it 2.271 r_angle_refined_deg 2.041 r_mcbond_it 1.659 r_rigid_bond_restr 1.552 r_nbtor_refined 0.319 r_nbd_refined 0.263 r_symmetry_hbond_refined 0.247 r_symmetry_vdw_refined 0.243 r_xyhbond_nbd_refined 0.214 r_chiral_restr 0.103 r_metal_ion_refined 0.054 r_symmetry_metal_ion_refined 0.043 r_bond_refined_d 0.015 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 760 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection XDS data reduction XSCALE data scaling PHASER phasing