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Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U1V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 292 11% (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 coefficient Solvent content 2.2 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.128 α = 90 b = 56.128 β = 90 c = 154.423 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2004-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 1.007 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.3 20 91.7 0.051 15.2 5 70364 63575 -3 32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.3 1.4 69.5 0.229 4.6 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION rigid body refinement of 1U1V THROUGHOUT 1U1V 1.3 19.1 61287 3287 91.77 0.13482 0.13344 0.1343 0.15973 0.1611 RANDOM 24.128
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 Key Refinement Restraint Deviation r_sphericity_free 10.969 r_scangle_it 7.409 r_dihedral_angle_1_deg 6.717 r_sphericity_bonded 6.67 r_scbond_it 5.095 r_angle_other_deg 3.938 r_mcangle_it 3.588 r_rigid_bond_restr 2.816 r_angle_refined_deg 2.714 r_mcbond_it 2.651
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 10.969 r_scangle_it 7.409 r_dihedral_angle_1_deg 6.717 r_sphericity_bonded 6.67 r_scbond_it 5.095 r_angle_other_deg 3.938 r_mcangle_it 3.588 r_rigid_bond_restr 2.816 r_angle_refined_deg 2.714 r_mcbond_it 2.651 r_symmetry_vdw_other 0.385 r_nbd_other 0.299 r_symmetry_hbond_refined 0.293 r_symmetry_vdw_refined 0.263 r_nbd_refined 0.242 r_xyhbond_nbd_refined 0.198 r_chiral_restr 0.177 r_nbtor_other 0.12 r_gen_planes_other 0.069 r_bond_refined_d 0.035 r_gen_planes_refined 0.027 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2209 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling