5K5B

Wild-type PAS-GAF fragment from Deinococcus radiodurans BphP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4Q0H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.95293sodium acetate, PEG 400, DTT, 2-methyl-2, 4-pentanediol
Crystal Properties
Matthews coefficientSolvent content
2.448.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.76α = 90
b = 54.28β = 92.2
c = 70.15γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.972957ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.3546.9798.10.0360.99918.374.3675872-325.092
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)
11.351.3895.70.562.314.23

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 REPLACEMENTTHROUGHOUT4Q0H1.3539.3772086379598.070.14220.14070.1709RANDOM25.474
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]
0.08-0.2-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.039
r_sphericity_free30.668
r_sphericity_bonded13.888
r_dihedral_angle_4_deg12.91
r_dihedral_angle_3_deg11.684
r_dihedral_angle_1_deg6.327
r_mcangle_it2.235
r_scbond_it2.134
r_mcbond_it1.675
r_rigid_bond_restr1.654
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.039
r_sphericity_free30.668
r_sphericity_bonded13.888
r_dihedral_angle_4_deg12.91
r_dihedral_angle_3_deg11.684
r_dihedral_angle_1_deg6.327
r_mcangle_it2.235
r_scbond_it2.134
r_mcbond_it1.675
r_rigid_bond_restr1.654
r_angle_refined_deg1.506
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2335
Nucleic Acid Atoms
Solvent Atoms322
Heterogen Atoms63

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction