3CBS

CELLULAR RETINOIC ACID BINDING PROTEIN II IN COMPLEX WITH A SYNTHETIC RETINOIC ACID (RO-12 7310)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.520% MONOMETHYL PEG 5000 0.2 M TRIS-HCL 0.2 M LICL , pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.4750.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.03α = 90
b = 48.32β = 90
c = 83.82γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATERIGAKUMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1

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
124591.90.02935.13.21005113.9
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)
122.0393.30.1112.23

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1CBS2101001682092.40.20.244RANDOM24.2
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]
-3.450.532.92
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d25.6
x_scangle_it2.82
x_scbond_it1.87
x_mcangle_it1.53
x_angle_deg1.5
x_mcbond_it0.94
x_improper_angle_d0.69
x_bond_d0.006
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d25.6
x_scangle_it2.82
x_scbond_it1.87
x_mcangle_it1.53
x_angle_deg1.5
x_mcbond_it0.94
x_improper_angle_d0.69
x_bond_d0.006
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1091
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms22

Software

Software
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling