5DFX

Structure of the parental state of GAF3 from Slr1393 of Synechocystis sp. PCC6803 (in vivo assembled protein/chromophore)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72850.02 M Tris pH 7.0, 0.1 M sodium chloride, 7.7 % (w/v) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.3848.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.12α = 90
b = 63.12β = 90
c = 118.83γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97916ESRFID29

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
11.819.9699.70.05619.196.6322947
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)
11.81.91990.3015.426.52

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.819.9621860103999.480.165850.164310.19902RANDOM27.946
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_deg32.319
r_dihedral_angle_4_deg20.042
r_dihedral_angle_3_deg12.336
r_long_range_B_refined7.58
r_long_range_B_other7.578
r_dihedral_angle_1_deg6.711
r_scangle_other5.776
r_mcangle_other4.17
r_mcangle_it4.163
r_scbond_it3.907
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.319
r_dihedral_angle_4_deg20.042
r_dihedral_angle_3_deg12.336
r_long_range_B_refined7.58
r_long_range_B_other7.578
r_dihedral_angle_1_deg6.711
r_scangle_other5.776
r_mcangle_other4.17
r_mcangle_it4.163
r_scbond_it3.907
r_scbond_other3.905
r_mcbond_it3.05
r_mcbond_other3.037
r_angle_refined_deg2.428
r_angle_other_deg1.032
r_chiral_restr0.144
r_bond_refined_d0.022
r_gen_planes_other0.017
r_gen_planes_refined0.014
r_bond_other_d0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1299
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling