2FS7

Crystal Structure of Apo-Cellular Retinoic Acid Binding Protein Type II At 1.55 Angstroms Resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829830% (w/v) PEG 8000, 0.1 M Tris-HCl pH 8.0, and 0.2 M Sodium Acetate, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.244.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.475α = 73.09
b = 37.22β = 75.74
c = 57.597γ = 87.22
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCH2005-04-01MSINGLE WAVELENGTH
21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B1.000APS14-ID-B

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
11.555092.30.04223.72.23896835956-318.7
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)
1.551.6168.168.10.1573.362

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 RefinementTHROUGHOUT1.55503595435954359592.450.1490.1490.1440.201RANDOM18.544
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]
-0.63-0.760.73-1.11-0.461.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.574
r_dihedral_angle_4_deg19.155
r_dihedral_angle_3_deg11.864
r_sphericity_free7.673
r_dihedral_angle_1_deg6.711
r_scangle_it4.916
r_scbond_it3.712
r_sphericity_bonded3.214
r_mcangle_it2.515
r_mcbond_it2.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.574
r_dihedral_angle_4_deg19.155
r_dihedral_angle_3_deg11.864
r_sphericity_free7.673
r_dihedral_angle_1_deg6.711
r_scangle_it4.916
r_scbond_it3.712
r_sphericity_bonded3.214
r_mcangle_it2.515
r_mcbond_it2.12
r_rigid_bond_restr2.081
r_angle_refined_deg1.742
r_angle_other_deg0.888
r_mcbond_other0.688
r_symmetry_vdw_other0.254
r_symmetry_vdw_refined0.241
r_nbd_refined0.199
r_nbd_other0.197
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.179
r_symmetry_hbond_refined0.17
r_chiral_restr0.113
r_nbtor_other0.086
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2163
Nucleic Acid Atoms
Solvent Atoms321
Heterogen Atoms13

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction