7DIG | pdb_00007dig

Green fluorescent protein from Dendronephthya sp. SSAL-2002


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5EXB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP295.15Tris, MgCl2, PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.2645.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.826α = 90
b = 124.737β = 90
c = 129.059γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 11C0.9794PAL/PLS11C

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
12.65095.50.13610.64.255239
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)
12.62.6489.30.3571.6

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 REPLACEMENTTHROUGHOUT5EXB2.648.752498270795.070.23640.23420.240.28130.24RANDOM39.75
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]
-0.190.58-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.238
r_dihedral_angle_3_deg21.408
r_dihedral_angle_4_deg19.038
r_dihedral_angle_1_deg7.87
r_angle_refined_deg1.634
r_angle_other_deg1.195
r_chiral_restr0.057
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.238
r_dihedral_angle_3_deg21.408
r_dihedral_angle_4_deg19.038
r_dihedral_angle_1_deg7.87
r_angle_refined_deg1.634
r_angle_other_deg1.195
r_chiral_restr0.057
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14264
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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