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Crystal structure of the extracellular domains of coxsackie & adenovirus receptor from mouse (mCAR)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EAJ 1EAJ (complete) for domain D1 2V5R (residues 5-40, 44-62, 68-76, 81-90) for domain D2 experimental model PDB 2V5R 1EAJ (complete) for domain D1 2V5R (residues 5-40, 44-62, 68-76, 81-90) for domain D2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 protein buffer:
20mM TRIS
50mM NaCl
protein concentration:
8mg / ml;
crystallization buffer
0.1M HEPES pH 7.5
21% PEG 4000
15% isopropanol;
crystalliztion setup:
mixture 400nl protein sample : 400nl crystallization buffer
reservoir filled with 80 ul crystallization buffer;
cryo solution:
25% PEG 4000
20% isopropanol
10% glycerol
0.1M HEPES pH 7.5
freezing of crystals: crystallization setup was overlayed with cryosolution, floating crystals were removed with a cryoloop and flash-frozen in liquid nitrogen., VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.98 58.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.369 α = 90 b = 61.468 β = 90 c = 86.355 γ = 90
Symmetry Space Group P 21 21 2
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 RAYONIX MX-225 Mirror 1: Silicon, active surface 50nm Rh-coated. Double crystal monochromator: Si-111 crystal. Mirror 2: Glas, active surface 50nm Rh-coated 2008-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 2.18 50 99.1 0.083 13.63 3.3 15245 47.774
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) 2.18 2.26 98.2 0.453 2.37 3.2 1481
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 1EAJ (complete) for domain D1
2V5R (residues 5-40, 44-62, 68-76, 81-90) for domain D2 2.19 50 15150 754 98.482 0.212 0.209 0.2178 0.265 0.2777 RANDOM 38.075
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] -0.45 1.14 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.734 r_dihedral_angle_4_deg 21.723 r_dihedral_angle_3_deg 16.335 r_dihedral_angle_1_deg 6.909 r_scangle_it 4.801 r_scbond_it 3.532 r_mcangle_it 2.098 r_mcbond_it 1.659 r_angle_refined_deg 1.483 r_angle_other_deg 0.871
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.734 r_dihedral_angle_4_deg 21.723 r_dihedral_angle_3_deg 16.335 r_dihedral_angle_1_deg 6.909 r_scangle_it 4.801 r_scbond_it 3.532 r_mcangle_it 2.098 r_mcbond_it 1.659 r_angle_refined_deg 1.483 r_angle_other_deg 0.871 r_mcbond_other 0.263 r_symmetry_vdw_other 0.229 r_nbd_refined 0.208 r_nbd_other 0.201 r_symmetry_vdw_refined 0.183 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.141 r_nbtor_other 0.092 r_chiral_restr 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1647 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 8
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling