4Z1W

CRYSTAL STRUCTURE OF MONOMERIC BACTERIOPHYTOCHROME mutant D207L Y263F From Synchrotron


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3S7Q3S7Q, 4O8G
experimental modelPDB 4O8G3S7Q, 4O8G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4293Crystals 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
2.2346.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.434α = 90
b = 53.34β = 90.91
c = 65.69γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2015-02-12MSINGLE 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
11.323.896.50.05233.27.7777418.8
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)
11.31.3594.30.3517.7

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 REPLACEMENTTHROUGHOUT3S7Q, 4O8G1.323.2273911382996.360.145310.144550.16019RANDOM16.698
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]
-0.47-0.710.59-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.835
r_sphericity_free21.125
r_dihedral_angle_4_deg12.679
r_dihedral_angle_3_deg12.353
r_dihedral_angle_1_deg6.383
r_sphericity_bonded4.376
r_long_range_B_refined1.778
r_long_range_B_other1.479
r_angle_refined_deg1.314
r_scangle_other1.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.835
r_sphericity_free21.125
r_dihedral_angle_4_deg12.679
r_dihedral_angle_3_deg12.353
r_dihedral_angle_1_deg6.383
r_sphericity_bonded4.376
r_long_range_B_refined1.778
r_long_range_B_other1.479
r_angle_refined_deg1.314
r_scangle_other1.05
r_rigid_bond_restr0.968
r_scbond_it0.945
r_scbond_other0.944
r_mcangle_it0.884
r_mcangle_other0.884
r_angle_other_deg0.871
r_mcbond_it0.752
r_mcbond_other0.751
r_chiral_restr0.069
r_bond_refined_d0.006
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 Atoms2389
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms86

Software

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