3JZ7

Crystal structure of the extracellular domains of coxsackie & adenovirus receptor from mouse (mCAR)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293.15protein 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 coefficientSolvent content
2.9858.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.369α = 90
b = 61.468β = 90
c = 86.355γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDRAYONIX MX-225Mirror 1: Silicon, active surface 50nm Rh-coated. Double crystal monochromator: Si-111 crystal. Mirror 2: Glas, active surface 50nm Rh-coated2008-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.185099.10.08313.633.31524547.774
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.182.2698.20.4532.373.21481

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1EAJ (complete) for domain D1 2V5R (residues 5-40, 44-62, 68-76, 81-90) for domain D22.19501515075498.4820.2120.2090.265RANDOM38.075
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]
-0.451.14-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.734
r_dihedral_angle_4_deg21.723
r_dihedral_angle_3_deg16.335
r_dihedral_angle_1_deg6.909
r_scangle_it4.801
r_scbond_it3.532
r_mcangle_it2.098
r_mcbond_it1.659
r_angle_refined_deg1.483
r_angle_other_deg0.871
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.734
r_dihedral_angle_4_deg21.723
r_dihedral_angle_3_deg16.335
r_dihedral_angle_1_deg6.909
r_scangle_it4.801
r_scbond_it3.532
r_mcangle_it2.098
r_mcbond_it1.659
r_angle_refined_deg1.483
r_angle_other_deg0.871
r_mcbond_other0.263
r_symmetry_vdw_other0.229
r_nbd_refined0.208
r_nbd_other0.201
r_symmetry_vdw_refined0.183
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.163
r_symmetry_hbond_refined0.141
r_nbtor_other0.092
r_chiral_restr0.091
r_bond_refined_d0.016
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1647
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms8

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling