4EDE

Crystal Structure of the Q108K:K40L:T51V:T53C:Y19W:R58W:T29L:A33W Mutant of Cellular Retinol Binding Protein Type II in Complex with All-trans-Retinal at 1.4 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
2.0840.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.348α = 90.04
b = 36.452β = 94.55
c = 64.265γ = 116.36
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDMARMOSAIC 300 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.97918APS21-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
11.432.6374982249822
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)
11.41.4293.50.3582.7

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 2RCQ1.432.6374429241479236893.650.201590.199440.24158RANDOM17.966
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.126
r_dihedral_angle_4_deg19.892
r_dihedral_angle_3_deg14.759
r_dihedral_angle_1_deg6.716
r_scangle_it6.223
r_scbond_it4.126
r_mcangle_it2.864
r_angle_refined_deg2.434
r_mcbond_it1.741
r_chiral_restr0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.126
r_dihedral_angle_4_deg19.892
r_dihedral_angle_3_deg14.759
r_dihedral_angle_1_deg6.716
r_scangle_it6.223
r_scbond_it4.126
r_mcangle_it2.864
r_angle_refined_deg2.434
r_mcbond_it1.741
r_chiral_restr0.17
r_bond_refined_d0.029
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2153
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms32

Software

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