2CBS

CELLULAR RETINOIC ACID BINDING PROTEIN II IN COMPLEX WITH A SYNTHETIC RETINOIC ACID (RO-13 6307)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.520% MONOMETHYL PEG 5000 0.1 M SODIUM ACETATE PH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.5952.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.25α = 90
b = 47.64β = 90
c = 74.83γ = 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
12.145.297.70.06125.94.3968311.3
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)
2.12.1597.70.1611.64.3

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 DIFFRACTIONOTHERTHROUGHOUT1CBS2.18945378097.20.20.233RANDOM22.3
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]
-3.29-0.643.93
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d25.3
x_scangle_it4.05
x_scbond_it2.63
x_mcangle_it2.19
x_angle_deg1.4
x_mcbond_it1.4
x_improper_angle_d0.69
x_bond_d0.007
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d25.3
x_scangle_it4.05
x_scbond_it2.63
x_mcangle_it2.19
x_angle_deg1.4
x_mcbond_it1.4
x_improper_angle_d0.69
x_bond_d0.007
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 Atoms53
Heterogen Atoms25

Software

Software
Software NamePurpose
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing