6FTD

Deinococcus radiodurans BphP PAS-GAF H290T mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.9529767 mM Sodium acetate, 3.3 % PEG400, 1mM DTT, 30% 2-methyl-2,4-pentanediol
Crystal Properties
Matthews coefficientSolvent content
2.2946.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.81α = 90
b = 53.03β = 93.3
c = 135.88γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2015-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.96770ESRFMASSIF-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.447.3399.70.1080.1240.9977.484.25132351-315.679
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4499.51.3621.5520.3360.934.26

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 REPLACEMENTTHROUGHOUT5K5B1.447.33125781662099.750.150460.147950.19816RANDOM24.18
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]
0.13-0.410.06-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.795
r_sphericity_free32.082
r_dihedral_angle_4_deg14.657
r_sphericity_bonded13.416
r_dihedral_angle_3_deg13.334
r_dihedral_angle_1_deg6.958
r_long_range_B_refined6.368
r_scangle_other6.16
r_long_range_B_other6.112
r_scbond_it5.569
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.795
r_sphericity_free32.082
r_dihedral_angle_4_deg14.657
r_sphericity_bonded13.416
r_dihedral_angle_3_deg13.334
r_dihedral_angle_1_deg6.958
r_long_range_B_refined6.368
r_scangle_other6.16
r_long_range_B_other6.112
r_scbond_it5.569
r_scbond_other5.569
r_mcangle_it5.401
r_mcangle_other5.4
r_rigid_bond_restr5.167
r_mcbond_it4.745
r_mcbond_other4.719
r_angle_refined_deg2.551
r_angle_other_deg1.219
r_chiral_restr0.155
r_bond_refined_d0.028
r_gen_planes_refined0.015
r_bond_other_d0.002
r_gen_planes_other0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4790
Nucleic Acid Atoms
Solvent Atoms573
Heterogen Atoms126

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement