5M82

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5M85 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.52770.1 M NaCl, 0.1 M CAPSO pH 9.5, 0.175 M LiSO4, 14% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.3547.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.286α = 90
b = 75.286β = 90
c = 71.38γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-FKB mirrors2015-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.976252PETRA 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
11.8665.294.40.027125.793.8918191
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)
11.861.9878.90.923.373.07

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 REPLACEMENTTHROUGHOUT5M851.8665.21726392194.330.195960.19410.22872RANDOM38.426
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]
0.530.260.53-1.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.767
r_dihedral_angle_4_deg15.857
r_dihedral_angle_3_deg12.798
r_long_range_B_other8.055
r_long_range_B_refined8.03
r_dihedral_angle_1_deg6.737
r_scangle_other6.544
r_scbond_it4.414
r_scbond_other4.411
r_mcangle_it4.394
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.767
r_dihedral_angle_4_deg15.857
r_dihedral_angle_3_deg12.798
r_long_range_B_other8.055
r_long_range_B_refined8.03
r_dihedral_angle_1_deg6.737
r_scangle_other6.544
r_scbond_it4.414
r_scbond_other4.411
r_mcangle_it4.394
r_mcangle_other4.393
r_mcbond_it3.492
r_mcbond_other3.49
r_angle_refined_deg2.376
r_angle_other_deg1.48
r_chiral_restr0.144
r_bond_refined_d0.02
r_gen_planes_other0.02
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 Atoms1304
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing