4ZRR

Crystal Structure of Monomeric Bacteriophytochrome mutant D207L Y263F at 1.5 A resolution Using a home source.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4O8G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4298Crystals of D207L-Y263F phytochrome mutant were grown from hanging drop vapor diffusion in 20% PEG400, starting protein concentration of 20 mg/ml, and 0.1M phosphate citrate buffer at pH 4.0.
Crystal Properties
Matthews coefficientSolvent content
2.4551.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.819α = 90
b = 55.046β = 91.89
c = 69.797γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 60002015-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
11.547.6960.0514.692.95486410.84
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)
11.51.5591.20.1794.834

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4O8G1.52552043270995.90.1620.160.195RANDOM18.84
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]
0.04-0.030.08-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.317
r_sphericity_free27.097
r_dihedral_angle_3_deg13.078
r_dihedral_angle_4_deg9.571
r_sphericity_bonded6.543
r_dihedral_angle_1_deg6.303
r_long_range_B_refined2.59
r_long_range_B_other2.59
r_mcangle_it1.398
r_mcangle_other1.398
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.317
r_sphericity_free27.097
r_dihedral_angle_3_deg13.078
r_dihedral_angle_4_deg9.571
r_sphericity_bonded6.543
r_dihedral_angle_1_deg6.303
r_long_range_B_refined2.59
r_long_range_B_other2.59
r_mcangle_it1.398
r_mcangle_other1.398
r_scangle_other1.394
r_angle_refined_deg1.389
r_scbond_it1.199
r_scbond_other1.199
r_mcbond_it1.1
r_mcbond_other1.096
r_angle_other_deg1.026
r_rigid_bond_restr0.999
r_chiral_restr0.123
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2362
Nucleic Acid Atoms
Solvent Atoms288
Heterogen Atoms105

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SAINTdata scaling
PHASERphasing