4Y5F

PAS-GAF fragment from Deinococcus radiodurans BphP assembled with BV - Y307S, high dose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.629610% PEG3350, 19% isopropanol, 5% glycerol, 100 mM citric acid/NaOH, ph 5.6
Crystal Properties
Matthews coefficientSolvent content
2.4249.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.274α = 90
b = 51.803β = 116.22
c = 80.272γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-08-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.1NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.75096.20.105256.833245
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)
11.71.7476.70.4591.82.9

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 REPLACEMENTTHROUGHOUTPDB entry 2O9C1.75033245176196.190.146430.142980.21393RANDOM28.207
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]
-0.490.240.56-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.283
r_sphericity_free21.846
r_dihedral_angle_4_deg19.197
r_dihedral_angle_3_deg13.95
r_sphericity_bonded13.881
r_scangle_other6.917
r_long_range_B_refined6.691
r_long_range_B_other6.691
r_dihedral_angle_1_deg6.431
r_scbond_it6.187
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.283
r_sphericity_free21.846
r_dihedral_angle_4_deg19.197
r_dihedral_angle_3_deg13.95
r_sphericity_bonded13.881
r_scangle_other6.917
r_long_range_B_refined6.691
r_long_range_B_other6.691
r_dihedral_angle_1_deg6.431
r_scbond_it6.187
r_scbond_other6.186
r_rigid_bond_restr6.052
r_mcangle_other5.807
r_mcangle_it5.801
r_mcbond_it4.976
r_mcbond_other4.95
r_angle_refined_deg2.043
r_angle_other_deg1.234
r_chiral_restr0.127
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_gen_planes_other0.004
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2403
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling