5L8M

Wild-type PAS-GAF fragment from Deinococcus radiodurans Bphp collected at LCLS


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE4.95283sodium acetate, DTT, 2-methyl-2,4-pentandiol, PEG400
Crystal Properties
Matthews coefficientSolvent content
2.4249.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.1α = 90
b = 54.8β = 92.6
c = 69.9γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELCS-PAD CXI-12016-01-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE CXI1.3SLAC LCLSCXI

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)R Split (All)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
12.138.299.970.980.09197.7781920853

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 REPLACEMENTTHROUGHOUT4Q0H2.138.21873295893.960.178110.17610.21827RANDOM42.92
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]
0.56-0.870.45-0.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.154
r_dihedral_angle_3_deg13.379
r_dihedral_angle_4_deg10.703
r_dihedral_angle_1_deg6.458
r_long_range_B_refined5.963
r_long_range_B_other5.963
r_scangle_other3.405
r_mcangle_other3.09
r_mcangle_it3.088
r_scbond_it2.022
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.154
r_dihedral_angle_3_deg13.379
r_dihedral_angle_4_deg10.703
r_dihedral_angle_1_deg6.458
r_long_range_B_refined5.963
r_long_range_B_other5.963
r_scangle_other3.405
r_mcangle_other3.09
r_mcangle_it3.088
r_scbond_it2.022
r_scbond_other2.021
r_mcbond_it1.85
r_mcbond_other1.83
r_angle_refined_deg1.313
r_angle_other_deg0.888
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms2333
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing