2G7B

Crystal Structure of the R132K:R111L:L121E mutant of Cellular Retinoic Acid Binding Protein Type II In Complex With All-Trans-Retinal At 1.18 Angstroms Resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.827718% (w/v) PEG 6000 and 0.1 M sodium acetate pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5952.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.459α = 90
b = 45.514β = 90
c = 77.747γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCH2004-06-19MSINGLE 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
11.184096.70.07225.65424152457-3
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)
1.181.2274.674.60.332

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 RefinementTHROUGHOUT1.1822.815240552405292096.710.130.130.1290.155RANDOM12.18
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]
0.310.2-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.278
r_dihedral_angle_4_deg10.899
r_dihedral_angle_3_deg10.44
r_sphericity_free9.638
r_dihedral_angle_1_deg7.047
r_scangle_it5.242
r_sphericity_bonded4.631
r_scbond_it3.668
r_mcangle_it2.866
r_rigid_bond_restr1.949
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.278
r_dihedral_angle_4_deg10.899
r_dihedral_angle_3_deg10.44
r_sphericity_free9.638
r_dihedral_angle_1_deg7.047
r_scangle_it5.242
r_sphericity_bonded4.631
r_scbond_it3.668
r_mcangle_it2.866
r_rigid_bond_restr1.949
r_mcbond_it1.917
r_angle_refined_deg1.795
r_angle_other_deg1.585
r_mcbond_other0.952
r_symmetry_vdw_refined0.417
r_metal_ion_refined0.362
r_nbd_refined0.333
r_symmetry_vdw_other0.288
r_nbd_other0.241
r_symmetry_hbond_refined0.21
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.173
r_chiral_restr0.122
r_nbtor_other0.088
r_bond_refined_d0.019
r_gen_planes_other0.011
r_gen_planes_refined0.01
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1146
Nucleic Acid Atoms
Solvent Atoms285
Heterogen Atoms22

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction