5M85

Three-dimensional structure of the intermediate state of GAF3 from Slr1393 of Synechocystis sp. PCC6803


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.52770.1 M NaCl, 0.1 M LiSO4, 0.1 M CAPSO pH 9.5, 12% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.3347.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.101α = 90
b = 75.101β = 90
c = 71.21γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-FKB mirrors2015-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.954PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)CC (Half)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
12.171.2199.60.063133.3420.0713390
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2398.20.9595.9619.2

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 REPLACEMENTTHROUGHOUT5DFX2.165.041275164099.760.172130.169710.22233RANDOM43.486
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]
-0.19-0.09-0.190.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.597
r_dihedral_angle_4_deg14.973
r_dihedral_angle_3_deg14.316
r_long_range_B_other8.744
r_long_range_B_refined8.715
r_scangle_other7.307
r_dihedral_angle_1_deg6.721
r_scbond_it5.098
r_scbond_other5.055
r_mcangle_it4.406
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.597
r_dihedral_angle_4_deg14.973
r_dihedral_angle_3_deg14.316
r_long_range_B_other8.744
r_long_range_B_refined8.715
r_scangle_other7.307
r_dihedral_angle_1_deg6.721
r_scbond_it5.098
r_scbond_other5.055
r_mcangle_it4.406
r_mcangle_other4.403
r_mcbond_it3.636
r_mcbond_other3.6
r_angle_refined_deg2.43
r_angle_other_deg1.294
r_chiral_restr0.122
r_bond_refined_d0.019
r_gen_planes_other0.018
r_gen_planes_refined0.013
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 Atoms1315
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing