1XUB

Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U1V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.429211% (w/v) PEG 3350, 0.1M Na Citrate, 0.2M (NH4)2 Sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.243.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.128α = 90
b = 56.128β = 90
c = 154.423γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-41.007ESRFID14-4

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
11.32091.70.05115.257036463575-332
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)
1.31.469.50.2294.63

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 DIFFRACTIONrigid body refinement of 1U1VTHROUGHOUT1U1V1.319.161287328791.770.134820.133440.15973RANDOM24.128
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free10.969
r_scangle_it7.409
r_dihedral_angle_1_deg6.717
r_sphericity_bonded6.67
r_scbond_it5.095
r_angle_other_deg3.938
r_mcangle_it3.588
r_rigid_bond_restr2.816
r_angle_refined_deg2.714
r_mcbond_it2.651
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free10.969
r_scangle_it7.409
r_dihedral_angle_1_deg6.717
r_sphericity_bonded6.67
r_scbond_it5.095
r_angle_other_deg3.938
r_mcangle_it3.588
r_rigid_bond_restr2.816
r_angle_refined_deg2.714
r_mcbond_it2.651
r_symmetry_vdw_other0.385
r_nbd_other0.299
r_symmetry_hbond_refined0.293
r_symmetry_vdw_refined0.263
r_nbd_refined0.242
r_xyhbond_nbd_refined0.198
r_chiral_restr0.177
r_nbtor_other0.12
r_gen_planes_other0.069
r_bond_refined_d0.035
r_gen_planes_refined0.027
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2209
Nucleic Acid Atoms
Solvent Atoms359
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling