2JA4

Crystal structure of CD5 domain III reveals the fold of a group B scavenger cysteine-rich receptor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.415-25% PEG 8000, 100 MM NAAC PH 4.4, 200 MM LI2SO4
Crystal Properties
Matthews coefficientSolvent content
3.767.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.931α = 90
b = 62.931β = 90
c = 72.564γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

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
12.215096.90.0515.35.4120982
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)
12.212.2695.60.242.24.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.2119.18789938795.60.1960.1930.248RANDOM44.77
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]
0.380.190.38-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.047
r_dihedral_angle_4_deg25.84
r_dihedral_angle_3_deg19.026
r_dihedral_angle_1_deg12.584
r_scangle_it9.823
r_scbond_it7.241
r_mcangle_it4.863
r_mcbond_it3.492
r_angle_refined_deg2.156
r_nbtor_refined0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.047
r_dihedral_angle_4_deg25.84
r_dihedral_angle_3_deg19.026
r_dihedral_angle_1_deg12.584
r_scangle_it9.823
r_scbond_it7.241
r_mcangle_it4.863
r_mcbond_it3.492
r_angle_refined_deg2.156
r_nbtor_refined0.33
r_nbd_refined0.259
r_xyhbond_nbd_refined0.215
r_chiral_restr0.183
r_symmetry_vdw_refined0.156
r_symmetry_hbond_refined0.141
r_bond_refined_d0.018
r_gen_planes_refined0.01
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms789
Nucleic Acid Atoms
Solvent Atoms58
Heterogen Atoms

Software

Software
Software NamePurpose
ARP/wARPmodel building
SCALEPACKdata scaling
BNPphasing
SHARPphasing
SOLOMONphasing
ARP/wARPphasing
REFMACrefinement