3D96

Crystal Structure of the R132K:Y134F Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.71 Angstroms Resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529830% (W/V) PEG 4000, 0.1 M TRIS-HCL, 0.2 M SODIUM ACETATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2645.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.59α = 73.9
b = 37.23β = 74.82
c = 58.77γ = 87.9
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCH2002-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 32-IDAPS32-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
11.75089.70.05220.442661721.8
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)
1.71.7648.90.241.55

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONRIGID BODY REFINEMENTTHROUGHOUT1.715025713229886.90.160.1530.222RANDOM28.7411
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]
-0.94-0.550.25-1.29-0.252.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.474
r_dihedral_angle_3_deg14.011
r_dihedral_angle_4_deg10.3
r_sphericity_free6.7
r_dihedral_angle_1_deg6.384
r_scangle_it3.669
r_scbond_it2.71
r_sphericity_bonded2.192
r_mcangle_it1.868
r_angle_refined_deg1.598
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.474
r_dihedral_angle_3_deg14.011
r_dihedral_angle_4_deg10.3
r_sphericity_free6.7
r_dihedral_angle_1_deg6.384
r_scangle_it3.669
r_scbond_it2.71
r_sphericity_bonded2.192
r_mcangle_it1.868
r_angle_refined_deg1.598
r_mcbond_it1.542
r_rigid_bond_restr1.352
r_angle_other_deg0.807
r_mcbond_other0.465
r_symmetry_vdw_other0.229
r_nbd_refined0.206
r_nbd_other0.192
r_symmetry_vdw_refined0.184
r_xyhbond_nbd_refined0.182
r_nbtor_refined0.179
r_symmetry_hbond_refined0.178
r_chiral_restr0.093
r_nbtor_other0.087
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2122
Nucleic Acid Atoms
Solvent Atoms362
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing