5LBR

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.95298Sodium Acetate, Peg400, 2-methyl-2,4-pentanediol
Crystal Properties
Matthews coefficientSolvent content
2.5752.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.22α = 90
b = 55.49β = 92.84
c = 71.63γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDMPCCD2015-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL30.987SACLABL3

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
12.271.541000.9760.1195.6281.218818
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.281000.6770.6824.1

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 REPLACEMENTTHROUGHOUT4Q0H2.271.54183899561000.180840.18210.2033RANDOM50.258
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]
0.36-0.760.44-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.627
r_dihedral_angle_3_deg13.566
r_dihedral_angle_4_deg12.759
r_long_range_B_refined6.758
r_long_range_B_other6.757
r_dihedral_angle_1_deg6.216
r_scangle_other4.406
r_mcangle_it3.599
r_mcangle_other3.599
r_scbond_it2.593
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.627
r_dihedral_angle_3_deg13.566
r_dihedral_angle_4_deg12.759
r_long_range_B_refined6.758
r_long_range_B_other6.757
r_dihedral_angle_1_deg6.216
r_scangle_other4.406
r_mcangle_it3.599
r_mcangle_other3.599
r_scbond_it2.593
r_scbond_other2.592
r_mcbond_it2.196
r_mcbond_other2.191
r_angle_refined_deg1.287
r_angle_other_deg0.913
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
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 Atoms2328
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
PHASERphasing
CrystFELdata scaling