3S7P

Crystal Structure of the Infrared Fluorescent D207H variant of Deinococcus Bacteriophytochrome chromophore binding domain at 1.72 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629814% v/v PEG 4000, 20% v/v isopropanol, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.K
Crystal Properties
Matthews coefficientSolvent content
2.1943.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.072α = 90
b = 51.666β = 115.33
c = 80.228γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrors2010-06-08MSINGLE 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 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
11.725098.50.03931.123.83426833621-318.8
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)
11.721.7597.30.2155.533.51642

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2O9C1.72243.193356431863170197.920.169010.169010.167530.19623RANDOM21.053
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]
-0.71-0.080.480.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.795
r_dihedral_angle_4_deg15.031
r_dihedral_angle_3_deg11.693
r_dihedral_angle_1_deg6.383
r_scangle_it3.243
r_scbond_it2.013
r_angle_refined_deg1.479
r_mcangle_it1.343
r_angle_other_deg0.959
r_mcbond_it0.742
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.795
r_dihedral_angle_4_deg15.031
r_dihedral_angle_3_deg11.693
r_dihedral_angle_1_deg6.383
r_scangle_it3.243
r_scbond_it2.013
r_angle_refined_deg1.479
r_mcangle_it1.343
r_angle_other_deg0.959
r_mcbond_it0.742
r_mcbond_other0.154
r_chiral_restr0.078
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2395
Nucleic Acid Atoms
Solvent Atoms298
Heterogen Atoms43

Software

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