7X2B | pdb_00007x2b

Red fluorescent protein from Diadumene lineata


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VK1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62933.0 M Ammonium Sulfate, 0.1 M Immidazole, 2.5 mg/mL protein
Crystal Properties
Matthews coefficientSolvent content
2.0740.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.929α = 90
b = 75.394β = 90
c = 118.955γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2021-06-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0000Photon FactoryBL-5A

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
11.6343.651000.068136.626779
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)
11.631.660.7882.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3vk11.6320.00126766139899.8660.1730.17110.180.20540.2123.948
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]
3.0360.328-3.364
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.063
r_dihedral_angle_4_deg17.302
r_dihedral_angle_3_deg14.127
r_dihedral_angle_1_deg7.304
r_lrange_it4.942
r_lrange_other4.904
r_scangle_it4.135
r_scangle_other4.129
r_scbond_it2.829
r_scbond_other2.827
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.063
r_dihedral_angle_4_deg17.302
r_dihedral_angle_3_deg14.127
r_dihedral_angle_1_deg7.304
r_lrange_it4.942
r_lrange_other4.904
r_scangle_it4.135
r_scangle_other4.129
r_scbond_it2.829
r_scbond_other2.827
r_mcangle_it2.404
r_mcangle_other2.403
r_mcbond_it1.817
r_mcbond_other1.817
r_angle_refined_deg1.674
r_angle_other_deg1.37
r_nbd_refined0.264
r_symmetry_nbd_refined0.261
r_nbd_other0.255
r_symmetry_nbd_other0.195
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.14
r_symmetry_xyhbond_nbd_refined0.117
r_symmetry_nbtor_other0.081
r_chiral_restr0.078
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1742
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHENIXrefinement