5O7M

Single-shot pink beam serial crystallography: Phycocyanin (One chip, chip_1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JBO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES6.4293PC was crystallized in 1.5 M Ammonium Sulfate solution, 25 mM MES pH 6.4. The protein crystals appear overnight in 1 mm inner diameter capillaries. The PC crystals size (30 to 40 um) is correlated to the protein concentration, which varied between 10-15 mg/ml.
Crystal Properties
Matthews coefficientSolvent content
2.7655.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 187.8α = 90
b = 187.8β = 90
c = 60.7γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDRAYONIX MX340-HS2016-07-09LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B1.15-1.25APS14-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.4610060.020.07347.5711.789313
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.462.5725.1611.83

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1JBO2.4614.9170.55890589259.940.14750.1420.1962Same as for 5MJP
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.017
f_angle_d0.83
f_chiral_restr0.034
f_bond_d0.004
f_plane_restr0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2498
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms129

Software

Software
Software NamePurpose
PHENIXrefinement
Precognitiondata reduction
PHASERphasing
Epinormdata reduction