4HE4

Crystal structure of the yellow fluorescent protein phiYFP (Phialidium sp.)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QY3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.16 M NaH2PO4 x 2H2O, 16% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.2845.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.87α = 90
b = 102.87β = 90
c = 242.53γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrorsMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

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
12.053099.70.078117.631372
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.1298.20.5627.13033

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 REPLACEMENTTHROUGHOUT1QY32.0528.731367158199.730.19890.19580.2557RANDOM41.3494
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
r_dihedral_angle_2_deg39.072
r_dihedral_angle_3_deg16.885
r_dihedral_angle_4_deg12.616
r_dihedral_angle_1_deg7.321
r_scangle_it4.623
r_scbond_it3.09
r_mcangle_it1.983
r_angle_refined_deg1.872
r_mcbond_it1.121
r_chiral_restr0.154
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.072
r_dihedral_angle_3_deg16.885
r_dihedral_angle_4_deg12.616
r_dihedral_angle_1_deg7.321
r_scangle_it4.623
r_scbond_it3.09
r_mcangle_it1.983
r_angle_refined_deg1.872
r_mcbond_it1.121
r_chiral_restr0.154
r_bond_refined_d0.026
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3650
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing