4QYP

The Crystal Structures of holo-wt human Cellular Retinol Binding protein II (hCRBPII) bound to Retinal


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2RCQPDB ENTRY 2RCQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION4.629830% PEG 4000, 0.1 M sodium acetate, 0.1 M ammonium acetate , pH 4.6, EVAPORATION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9938.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.44α = 107.75
b = 54.892β = 97.66
c = 68.716γ = 103.08
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDMARMOSAIC 300 mm CCD2007-09-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.0000APS21-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
11.625083.90.327687956034

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2RCQ1.6248.4456035300596.260.204310.201750.20.252450.25RANDOM21.059
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
r_dihedral_angle_2_deg36.733
r_dihedral_angle_4_deg19.16
r_dihedral_angle_3_deg14.397
r_dihedral_angle_1_deg7.285
r_scangle_it5.731
r_scbond_it3.743
r_mcangle_it2.549
r_angle_refined_deg2.2
r_mcbond_it1.542
r_chiral_restr0.156
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4307
Nucleic Acid Atoms
Solvent Atoms323
Heterogen Atoms83

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling