6T6K

Y201W mutant of the orange carotenoid protein from Synechocystis at pH 6.5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XB5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.52930.1M DL-Glutamic acid monohydrate; 0.1M DL-Alanine; 0.1M Glycine; 0.1M DL-Lysine monohydrochloride; 0.1M DL-Serine; 0.1M Imidazole; MES monohydrate (acid), pH 6.5; 20% v/v Ethylene glycol; 10 % w/v PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.3948.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.726α = 90
b = 82.726β = 90
c = 88.044γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.976250PETRA III, EMBL c/o DESYP14 (MX2)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.3744.021000.0470.99929.120.273479
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.371.391001.5320.81620.2

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 REPLACEMENTTHROUGHOUT4XB51.3737.5469781365499.930.13690.13540.1668RANDOM29.765
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]
0.70.350.7-2.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.803
r_dihedral_angle_4_deg20.265
r_rigid_bond_restr16.467
r_dihedral_angle_3_deg12.336
r_dihedral_angle_1_deg5.766
r_angle_other_deg1.526
r_angle_refined_deg1.357
r_chiral_restr0.078
r_bond_refined_d0.007
r_bond_other_d0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.803
r_dihedral_angle_4_deg20.265
r_rigid_bond_restr16.467
r_dihedral_angle_3_deg12.336
r_dihedral_angle_1_deg5.766
r_angle_other_deg1.526
r_angle_refined_deg1.357
r_chiral_restr0.078
r_bond_refined_d0.007
r_bond_other_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2343
Nucleic Acid Atoms
Solvent Atoms305
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing