7AA0

Structural comparison of cellular retinoic acid binding protein I and II in the presence and absence of natural and synthetic ligands


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OGB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP298PEG based
Crystal Properties
Matthews coefficientSolvent content
2.141.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.55α = 90
b = 49.92β = 96.03
c = 67.38γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PILATUS3 6M2018-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.8249.9297.60.0650.0890.0610.99610.43.523023
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.821.860.7351.0030.6780.4863.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5OGB1.8240.06423016112597.530.1990.19670.245229.068
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]
-0.0420.705-1.0620.934
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.454
r_dihedral_angle_3_deg14.034
r_dihedral_angle_4_deg14.029
r_dihedral_angle_1_deg7.953
r_lrange_it6.655
r_lrange_other6.633
r_scangle_it5.265
r_scangle_other5.264
r_mcangle_other3.303
r_mcangle_it3.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.454
r_dihedral_angle_3_deg14.034
r_dihedral_angle_4_deg14.029
r_dihedral_angle_1_deg7.953
r_lrange_it6.655
r_lrange_other6.633
r_scangle_it5.265
r_scangle_other5.264
r_mcangle_other3.303
r_mcangle_it3.3
r_scbond_other3.287
r_scbond_it3.286
r_mcbond_it2.296
r_mcbond_other2.292
r_angle_refined_deg1.55
r_angle_other_deg1.281
r_symmetry_xyhbond_nbd_refined0.308
r_symmetry_nbd_refined0.199
r_nbd_other0.191
r_xyhbond_nbd_refined0.19
r_nbd_refined0.186
r_symmetry_nbd_other0.183
r_nbtor_refined0.163
r_symmetry_nbtor_other0.086
r_chiral_restr0.072
r_symmetry_xyhbond_nbd_other0.015
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2178
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata reduction
PHASERphasing
Cootmodel building
XDSdata processing