4EEJ

Crystal Structure of the Q108K:K40L:T51V:T53C:Y19W:R58W:T29L:Q4R Mutant of Cellular Retinol Binding Protein Type II in Complex with All-trans-Retinal at 1.5 Angstrom Resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION, RECRYSTALLIZATION4.629840% PEG4000, 0.1 M sodium acetate trihydrate, pH 4.6, 0.1 M ammonium acetate, EVAPORATION, RECRYSTALLIZATION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0540.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.918α = 86.4
b = 35.756β = 86.44
c = 64.376γ = 64.94
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDMARMOSAIC 300 mm CCDmirrorMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.1272APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.50132.363976939769

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2RCQ1.50132.363595534239191795.230.172620.170650.20798RANDOM16.834
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_deg32.88
r_dihedral_angle_4_deg20.306
r_dihedral_angle_3_deg13.175
r_dihedral_angle_1_deg7.412
r_scangle_it6.115
r_scbond_it3.986
r_mcangle_it2.81
r_angle_refined_deg2.389
r_mcbond_it1.678
r_chiral_restr0.153
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.88
r_dihedral_angle_4_deg20.306
r_dihedral_angle_3_deg13.175
r_dihedral_angle_1_deg7.412
r_scangle_it6.115
r_scbond_it3.986
r_mcangle_it2.81
r_angle_refined_deg2.389
r_mcbond_it1.678
r_chiral_restr0.153
r_bond_refined_d0.027
r_gen_planes_refined0.016
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2156
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms48

Software

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