1U1W

Structure and function of phenazine-biosynthesis protein PhzF from Pseudomonas fluorescens 2-79


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U1VPDB entry 1u1v

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6293preincubation with ligand, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0439.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.6α = 90
b = 99.86β = 90
c = 57γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-41.00133ESRFID14-4

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
11.352099.70.06811.34116176116176320
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)
11.351.4599.30.4153.13.7

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 REPLACEMENTTHROUGHOUTPDB entry 1u1v1.3519.73110280584499.710.120050.118440.1503RANDOM12.061
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]
0.41-0.34-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free10.385
r_dihedral_angle_1_deg6.437
r_scangle_it5.934
r_sphericity_bonded4.349
r_scbond_it4.225
r_mcangle_it3.004
r_rigid_bond_restr2.405
r_mcbond_it2.258
r_angle_refined_deg2.058
r_angle_other_deg1.756
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free10.385
r_dihedral_angle_1_deg6.437
r_scangle_it5.934
r_sphericity_bonded4.349
r_scbond_it4.225
r_mcangle_it3.004
r_rigid_bond_restr2.405
r_mcbond_it2.258
r_angle_refined_deg2.058
r_angle_other_deg1.756
r_symmetry_vdw_other0.36
r_nbd_other0.282
r_symmetry_hbond_refined0.263
r_nbd_refined0.254
r_symmetry_vdw_refined0.225
r_xyhbond_nbd_refined0.213
r_chiral_restr0.149
r_nbtor_other0.089
r_gen_planes_other0.068
r_bond_other_d0.067
r_gen_planes_refined0.04
r_bond_refined_d0.026
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4248
Nucleic Acid Atoms
Solvent Atoms679
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDdata reduction
XDSdata scaling
MOLREPphasing