Experiment: 2FR3

 2FR3

Crystal Structure of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinoic Acid at 1.48 Angstroms Resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.429830% (w/v) PEG 4000, 0.1 M sodium citrate/citric acid pH 5.4, and 0.2 ammonium acetate (crystallization performed in dark room and under red light), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5551.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.287α = 90
b = 46.464β = 90
c = 77.261γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCH2005-07-23MSINGLE WAVELENGTH
21x-rayM
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 32-ID1.000APS32-ID

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
1,21.4839.8195.50.04428.19273322609017.1
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)
1.481.5396.496.40.1395.08

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONRigid Body RefinementTHROUGHOUT1.4839.812352323523262295.130.1310.1310.1260.174RANDOM15.735
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]
0.450.37-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.653
r_dihedral_angle_3_deg11.911
r_dihedral_angle_4_deg9.076
r_sphericity_free9.057
r_dihedral_angle_1_deg6.374
r_scangle_it5.001
r_sphericity_bonded4.394
r_scbond_it3.862
r_mcangle_it2.875
r_mcbond_it2.355
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1101
Nucleic Acid Atoms
Solvent Atoms228
Heterogen Atoms26

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction