2RCQ

Crystal structure of human apo Cellular Retinol Binding Protein II (CRBP-II)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OPAPDB ENTRY 1OPA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62930.1 M sodium citrate, 0.2 M sodium/potassium tartrate, 1.4 M ammonium sulphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
238.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.518α = 90
b = 49.834β = 90
c = 74.398γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmDOUBLE CRYSTAL (SI111, SI220) THREE-SEGMENT PT-COATED TOROIDAL MIRRORS2006-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.0ELETTRA5.2R

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
11.227960.0470.04718.9440046
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)
11.21.2395.40.1870.187845747

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 DIFFRACTIONTHROUGHOUTPDB ENTRY 1OPA1.2253799340021202895.110.1970.1970.1960.217RANDOM9.582
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]
0.29-0.12-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.983
r_dihedral_angle_3_deg12.69
r_dihedral_angle_4_deg11.854
r_dihedral_angle_1_deg6.683
r_scangle_it1.875
r_mcangle_it1.697
r_scbond_it1.238
r_mcbond_it1.176
r_angle_refined_deg1.044
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.983
r_dihedral_angle_3_deg12.69
r_dihedral_angle_4_deg11.854
r_dihedral_angle_1_deg6.683
r_scangle_it1.875
r_mcangle_it1.697
r_scbond_it1.238
r_mcbond_it1.176
r_angle_refined_deg1.044
r_nbtor_refined0.309
r_nbd_refined0.192
r_symmetry_vdw_refined0.154
r_symmetry_hbond_refined0.095
r_xyhbond_nbd_refined0.077
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_chiral_restr
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1158
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing