5OGB

Human Cellular Retinoic Acid Binding Protein II (CRABPII) with bound synthetic retinoid DC360.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FR3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293PEG 4000, Na Acetate
Crystal Properties
Matthews coefficientSolvent content
1.7128.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.05α = 90
b = 45.58β = 102.87
c = 36.67γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I021.0388DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.835.7791.16.22.69030

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 REPLACEMENTTHROUGHOUT2FR31.835.77855446890.560.176750.173410.23582RANDOM22.969
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]
3.980.13-1.57-2.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.927
r_dihedral_angle_4_deg17.446
r_dihedral_angle_3_deg15.025
r_long_range_B_refined7.569
r_long_range_B_other7.541
r_dihedral_angle_1_deg6.393
r_scangle_other3.846
r_mcangle_other2.792
r_mcangle_it2.79
r_scbond_other2.359
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.927
r_dihedral_angle_4_deg17.446
r_dihedral_angle_3_deg15.025
r_long_range_B_refined7.569
r_long_range_B_other7.541
r_dihedral_angle_1_deg6.393
r_scangle_other3.846
r_mcangle_other2.792
r_mcangle_it2.79
r_scbond_other2.359
r_scbond_it2.357
r_mcbond_it1.751
r_mcbond_other1.745
r_angle_refined_deg1.681
r_angle_other_deg0.962
r_chiral_restr0.097
r_bond_refined_d0.014
r_gen_planes_refined0.007
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 Atoms1078
Nucleic Acid Atoms
Solvent Atoms62
Heterogen Atoms26

Software

Software
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling
BUCCANEERmodel building
Cootmodel building
REFMACrefinement