2RCT

Crystal structure of human holo cellular retinol-binding protein II (CRBP-II)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62930.1 M sodium citrate, 0.2 M sodium/potassium tartrate, 1.4 M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9938.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.45α = 90
b = 49.966β = 90
c = 74.296γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210Diamond (111) monochromator2007-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.98ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.228.997.80.0630.06315.85.541159
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.21.2386.10.390.393.43.65179

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2RCQ1.2253903039030206597.720.1940.194080.192940.21542RANDOM10.603
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]
0.5-0.32-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.802
r_dihedral_angle_3_deg12.344
r_dihedral_angle_4_deg11.854
r_dihedral_angle_1_deg6.474
r_scangle_it1.843
r_mcangle_it1.551
r_scbond_it1.182
r_angle_refined_deg1.054
r_mcbond_it0.949
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.802
r_dihedral_angle_3_deg12.344
r_dihedral_angle_4_deg11.854
r_dihedral_angle_1_deg6.474
r_scangle_it1.843
r_mcangle_it1.551
r_scbond_it1.182
r_angle_refined_deg1.054
r_mcbond_it0.949
r_nbtor_refined0.312
r_nbd_refined0.197
r_symmetry_vdw_refined0.144
r_symmetry_hbond_refined0.101
r_xyhbond_nbd_refined0.088
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms1158
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
XFITdata reduction