5JFB

Crystal structure of the scavenger receptor cysteine-rich domain 5 (SRCR5) from porcine CD163


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BY2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.629825% (w/v) PEG 4000, 200mM (NH4)2SO4 in 100mM sodium acetate at pH 4.6
Crystal Properties
Matthews coefficientSolvent content
1.9938.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 29.711α = 90
b = 73.93β = 90
c = 87.527γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CMOSPilatus2015-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.979SSRFBL19U1

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
125097.10.10717.7106682
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.07

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 REPLACEMENTTHROUGHOUT1BY2243.76622331995.310.209220.207670.23905RANDOM23.6
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]
-0.360.160.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.554
r_dihedral_angle_4_deg18.415
r_dihedral_angle_3_deg13.139
r_dihedral_angle_1_deg7.337
r_long_range_B_refined4.212
r_long_range_B_other4.175
r_scangle_other2.242
r_mcangle_it1.744
r_mcangle_other1.743
r_scbond_it1.391
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.554
r_dihedral_angle_4_deg18.415
r_dihedral_angle_3_deg13.139
r_dihedral_angle_1_deg7.337
r_long_range_B_refined4.212
r_long_range_B_other4.175
r_scangle_other2.242
r_mcangle_it1.744
r_mcangle_other1.743
r_scbond_it1.391
r_scbond_other1.383
r_angle_refined_deg1.276
r_mcbond_other1.047
r_mcbond_it1.046
r_angle_other_deg0.92
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms761
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data processing
HKL-3000data scaling