3S7Q

Crystal Structure of a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.22983% v/v PEG 1000, 20% v/v ethanol, 6% v/v glycerol, 0.1M phosphate citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4950.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.129α = 90
b = 55.072β = 92.23
c = 69.969γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrors2011-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.9785APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.7483099.20.0622.13.63672236431
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.7481.791000.2254.73.6

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 2O9C1.74827.653643134609182299.180.188810.187340.21693RANDOM18.75
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]
-0.01-0.10.04-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.417
r_dihedral_angle_4_deg15.036
r_dihedral_angle_3_deg12.202
r_dihedral_angle_1_deg6.188
r_scangle_it2.416
r_angle_refined_deg1.552
r_scbond_it1.42
r_mcangle_it1.199
r_angle_other_deg0.965
r_mcbond_it0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.417
r_dihedral_angle_4_deg15.036
r_dihedral_angle_3_deg12.202
r_dihedral_angle_1_deg6.188
r_scangle_it2.416
r_angle_refined_deg1.552
r_scbond_it1.42
r_mcangle_it1.199
r_angle_other_deg0.965
r_mcbond_it0.64
r_chiral_restr0.074
r_mcbond_other0.062
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2364
Nucleic Acid Atoms
Solvent Atoms316
Heterogen Atoms103

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling