2O9B

Crystal Structure of Bacteriophytochrome chromophore binding domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62980.095 M sodium citrate, 19% v/v isopropanol, 19% v/v PEG 4000, 5% V/V glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2545.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.5α = 90
b = 51.5β = 116.4
c = 80.8γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER PROTEUMBruker Montel mirrors2005-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR

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
12.152496.40.104106.21813717484-3
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)
12.152.2378.80.3332.72.6

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1ZTU without chromophore or his tag2.1523.71174591653992096.50.19110.188520.23695RANDOM32.353
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]
-1.15-0.120.760.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.565
r_dihedral_angle_4_deg18.19
r_dihedral_angle_3_deg14.453
r_dihedral_angle_1_deg6.274
r_scangle_it3.003
r_scbond_it1.917
r_angle_refined_deg1.806
r_mcangle_it1.268
r_mcbond_it0.796
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.565
r_dihedral_angle_4_deg18.19
r_dihedral_angle_3_deg14.453
r_dihedral_angle_1_deg6.274
r_scangle_it3.003
r_scbond_it1.917
r_angle_refined_deg1.806
r_mcangle_it1.268
r_mcbond_it0.796
r_nbtor_refined0.3
r_symmetry_hbond_refined0.249
r_symmetry_vdw_refined0.217
r_nbd_refined0.212
r_xyhbond_nbd_refined0.153
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2394
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms43

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
HKL-2000data reduction