4JGE

Crystal structure of red fluorescent gene-engineered variant with improved folding - lanRFP_delS83 (Branchiostoma lanceolatum)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JF9PDB ENTRY 4JF9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729335.6 mg/ml of lanRFP- S83 in 20 mM Tris pH 8.0, 200 mM NaCl, 5 mM EDTA mixed with an equal amount of reservoir solution - 0.2M Na2HPO4 0.1M Tris pH 7.0 20% PEG3350 , VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
3.9368.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.762α = 90
b = 133.762β = 90
c = 156.956γ = 120
Symmetry
Space GroupP 64 2 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
11.943097.20.1097.9460055
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)
11.942.0189.10.4253.95388

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4JF91.9422.7659838121196.980.15660.15570.1982RANDOM20.5401
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_deg37.573
r_dihedral_angle_4_deg22.337
r_dihedral_angle_3_deg14.048
r_dihedral_angle_1_deg7.039
r_scangle_it5.892
r_scbond_it3.869
r_mcangle_it2.491
r_angle_refined_deg2.332
r_mcbond_it1.504
r_chiral_restr0.237
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.573
r_dihedral_angle_4_deg22.337
r_dihedral_angle_3_deg14.048
r_dihedral_angle_1_deg7.039
r_scangle_it5.892
r_scbond_it3.869
r_mcangle_it2.491
r_angle_refined_deg2.332
r_mcbond_it1.504
r_chiral_restr0.237
r_bond_refined_d0.033
r_gen_planes_refined0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3479
Nucleic Acid Atoms
Solvent Atoms495
Heterogen Atoms6

Software

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