3D95

Crystal Structure of the R132K:Y134F:R111L:L121E:T54V Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.20 Angstroms Resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.829820% (W/V) PEG 6000, 0.1 M SODIUM ACETATE, 5% ETHANOL, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2144.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.591α = 73.28
b = 36.897β = 75.91
c = 57.811γ = 87.76
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCH2004-03-02MSINGLE 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
11.24093.80.06618.177734716.6
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)
1.21.2489.90.2712.55

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 REFINEMENTTHROUGHOUT1.240752967560900.1410.1380.176RANDOM18.14
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]
-0.44-0.09-0.21-0.230.150.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.908
r_dihedral_angle_4_deg14.684
r_dihedral_angle_3_deg9.7
r_sphericity_free8.028
r_dihedral_angle_1_deg6.459
r_scangle_it4.873
r_sphericity_bonded4.865
r_scbond_it3.677
r_mcangle_it2.777
r_mcbond_it2.398
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.908
r_dihedral_angle_4_deg14.684
r_dihedral_angle_3_deg9.7
r_sphericity_free8.028
r_dihedral_angle_1_deg6.459
r_scangle_it4.873
r_sphericity_bonded4.865
r_scbond_it3.677
r_mcangle_it2.777
r_mcbond_it2.398
r_rigid_bond_restr2.397
r_angle_refined_deg1.676
r_mcbond_other0.936
r_angle_other_deg0.878
r_symmetry_vdw_other0.257
r_symmetry_vdw_refined0.24
r_nbd_refined0.207
r_nbd_other0.187
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.172
r_symmetry_hbond_refined0.159
r_chiral_restr0.112
r_nbtor_other0.086
r_bond_refined_d0.017
r_gen_planes_refined0.008
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 Atoms2174
Nucleic Acid Atoms
Solvent Atoms415
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing