6DD6

Crystal structure of bacterial (6-4) photolyase PhrB from in situ serial Laue diffraction


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH5.62941.7 mg/mL protein, 9-13% PEG 4000, 6% isopropanol, and 50 mM sodium citrate buffer at pH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.5852.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.7α = 90
b = 106.8β = 90
c = 57.3γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray294CCDRAYONIX MX340-HSKB mirrors2016-02-11LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B1-1.25APS14-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.310099.320.915.22773032.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.496.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4dja2.349.680.1627623138899.050.16930.16580.2347
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.382
f_angle_d1.127
f_chiral_restr0.054
f_bond_d0.009
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4107
Nucleic Acid Atoms
Solvent Atoms288
Heterogen Atoms84

Software

Software
Software NamePurpose
PHENIXrefinement
Precognitiondata reduction
Epinormdata reduction