3ZXS

Cryptochrome B from Rhodobacter sphaeroides


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.50.3 M MGCL2, 0.1M BICINE PH 8.5, 29.5% PEG2000, 17.5% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
4.1770.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.84α = 90
b = 137.84β = 90
c = 521.94γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rTORODIAL FOCUSING MIRROR2009-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.72599.80.126.915.281535-348.5
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)
12.72.7799.80.565.415.2

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 DIFFRACTIONSADTHROUGHOUTNONE2.724.957953520001000.198510.197740.22837SHELLED32.223
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]
1.630.821.63-2.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.948
r_dihedral_angle_4_deg21.181
r_dihedral_angle_3_deg17.039
r_dihedral_angle_1_deg6.15
r_scangle_it4.076
r_scbond_it2.383
r_mcangle_it1.586
r_angle_refined_deg1.546
r_angle_other_deg1.101
r_mcbond_it0.793
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.948
r_dihedral_angle_4_deg21.181
r_dihedral_angle_3_deg17.039
r_dihedral_angle_1_deg6.15
r_scangle_it4.076
r_scbond_it2.383
r_mcangle_it1.586
r_angle_refined_deg1.546
r_angle_other_deg1.101
r_mcbond_it0.793
r_mcbond_other0.206
r_chiral_restr0.088
r_bond_refined_d0.016
r_gen_planes_refined0.007
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11977
Nucleic Acid Atoms
Solvent Atoms417
Heterogen Atoms258

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing