4O01

Crystal Structure of D. radiodurans Bacteriophytochrome Photosensory Core Module in its Illuminated Form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2O9CPDB ENTRY 2O9C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52980.1M Tris, 0.2M NaCl, 25% PEG 3350, sequential 655nm illumination, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
4.2370.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.9α = 90
b = 195.7β = 90
c = 225γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2013-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.98043ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
13.2449.2299.90.2410.2489.6919.316196161928-3118.652
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.243.321004.394.5010.8320.34495

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2O9C3.2449.226185358759309499.950.2340.2340.232650.25972RANDOM158.6115
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]
5.55-1.75-3.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.587
r_dihedral_angle_3_deg15.249
r_dihedral_angle_4_deg10.871
r_mcangle_it9.369
r_mcbond_it5.78
r_mcbond_other5.778
r_dihedral_angle_1_deg5.402
r_angle_refined_deg1.159
r_angle_other_deg0.703
r_chiral_restr0.052
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.587
r_dihedral_angle_3_deg15.249
r_dihedral_angle_4_deg10.871
r_mcangle_it9.369
r_mcbond_it5.78
r_mcbond_other5.778
r_dihedral_angle_1_deg5.402
r_angle_refined_deg1.159
r_angle_other_deg0.703
r_chiral_restr0.052
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14784
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms172

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling