7ZTQ

Crystal structure of the carotenoid-binding protein domain from silkworm Bombyx mori (BmCBP) in the apoform


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5I9J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2885% v/v Tacsimate, pH 7.0, 0.1 M HEPES, pH 7.0, 10% w/v Polyethylene glycol monomethyl ether 5000
Crystal Properties
Matthews coefficientSolvent content
2.3647.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.911α = 90
b = 67.326β = 90
c = 121.637γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.873128ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.4547.199.70.0390.0430.017120.76.347986
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.4894.81.1241.2670.5690.4974.6

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5I9J1.4547.145518242899.660.14580.14330.1931RANDOM25.92
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]
0.79-0.33-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.706
r_dihedral_angle_2_deg10.482
r_dihedral_angle_1_deg7.949
r_rigid_bond_restr5.597
r_angle_refined_deg2.196
r_angle_other_deg1.499
r_chiral_restr0.127
r_gen_planes_refined0.016
r_bond_refined_d0.014
r_bond_other_d0.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.706
r_dihedral_angle_2_deg10.482
r_dihedral_angle_1_deg7.949
r_rigid_bond_restr5.597
r_angle_refined_deg2.196
r_angle_other_deg1.499
r_chiral_restr0.127
r_gen_planes_refined0.016
r_bond_refined_d0.014
r_bond_other_d0.014
r_gen_planes_other0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1862
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms6

Software

Software
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction