6LI1

Crystal structure of GPR52 ligand free form with flavodoxin fusion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelRosetta modelling

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE52930.1 M potassium acetate, 0.1 M sodium citrate pH 5.0, and 30% PEG400
Crystal Properties
Matthews coefficientSolvent content
3.9869.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.648α = 90
b = 79.891β = 90
c = 148.304γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.000SPring-8BL41XU

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
12.95097.60.2350.99111.89.218312
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)
12.932.7480.40.98

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTRosetta modelling2.928.431646291295.560.245480.244270.240.266770.27RANDOM78.363
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]
0.98-0.66-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.657
r_long_range_B_refined25.811
r_long_range_B_other25.811
r_scangle_other22.484
r_mcangle_it20.066
r_mcangle_other20.064
r_dihedral_angle_4_deg19.31
r_scbond_it17.212
r_scbond_other17.207
r_dihedral_angle_3_deg17.046
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3339
Nucleic Acid Atoms
Solvent Atoms7
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing