4ZH9

Crystal Structure of the Domain-Swapped Dimer Wild-Type of Human Cellular Retinol Binding Protein II


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2RCT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.529825% PEG 4000 (40%), 0.1M Sodium Acetate pH 4.5, Ammonium Acetate 0.1M
Crystal Properties
Matthews coefficientSolvent content
2.2946.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.851α = 90
b = 60.544β = 90
c = 64.021γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2014-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.978APS21-ID-D

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
12.665099.70.0592.415.94455
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)
12.663.041000.731

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTNONE2RCT2.6643.9891.36441745099.590.20750.20.2736
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.281
f_angle_d0.472
f_chiral_restr0.016
f_bond_d0.002
f_plane_restr0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1075
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing