7ZTR

Crystal structure of the carotenoid-binding protein domain from silkworm Bombyx mori (BmCBP) in the apoform, W232F mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7ZTQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2880.5 M Sodium citrate tribasic dihydrate, 0.1 M BIS- TRIS propane, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.1943.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.033α = 90
b = 66.772β = 90
c = 120.502γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2021-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54184

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
11.7560.2598.50.0860.090.0270.97920.811.525252
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)
11.751.7884.80.8480.9520.4180.6094.8

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 REPLACEMENTTHROUGHOUT7ZTQ1.7560.2524006120998.420.18360.18110.2323RANDOM22.825
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]
0.42-0.670.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg22.511
r_dihedral_angle_3_deg15.334
r_dihedral_angle_1_deg7.54
r_angle_refined_deg2.092
r_angle_other_deg0.873
r_chiral_restr0.137
r_bond_refined_d0.015
r_gen_planes_refined0.013
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1817
Nucleic Acid Atoms
Solvent Atoms179
Heterogen Atoms

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction