2G78

Crystal Structure of the R132K:Y134F Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinoic Acid at 1.70 Angstroms Resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.82980.1 M sodium citrate pH 4.8, 20% PEG 5000 and 10% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5852.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.702α = 90
b = 46.251β = 90
c = 77.553γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCH2003-01-12MSINGLE WAVELENGTH
21
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
11.74095.60.04617.661835917545-324.6
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)
1.71.7660.560.50.3611.91

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 RefinementTHROUGHOUT1.739.721703017030160693.020.1510.1510.1450.203RANDOM21.266
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]
-0.120.9-0.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.081
r_dihedral_angle_3_deg11.589
r_sphericity_free8.647
r_dihedral_angle_4_deg7.567
r_dihedral_angle_1_deg6.753
r_scangle_it4.479
r_sphericity_bonded3.618
r_scbond_it3.179
r_mcangle_it2.402
r_angle_refined_deg1.675
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.081
r_dihedral_angle_3_deg11.589
r_sphericity_free8.647
r_dihedral_angle_4_deg7.567
r_dihedral_angle_1_deg6.753
r_scangle_it4.479
r_sphericity_bonded3.618
r_scbond_it3.179
r_mcangle_it2.402
r_angle_refined_deg1.675
r_rigid_bond_restr1.641
r_mcbond_it1.62
r_angle_other_deg0.811
r_mcbond_other0.752
r_metal_ion_refined0.301
r_symmetry_vdw_other0.23
r_nbd_refined0.2
r_nbd_other0.193
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.16
r_symmetry_vdw_refined0.159
r_symmetry_hbond_refined0.159
r_chiral_restr0.093
r_nbtor_other0.084
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1101
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms23

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction