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Structure and function of phenazine-biosynthesis protein PhzF from Pseudomonas fluorescens 2-79
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U1V PDB entry 1u1v
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 preincubation with ligand, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.04 39.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.6 α = 90 b = 99.86 β = 90 c = 57 γ = 90
Symmetry Space Group P 21 21 2
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 2003-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 1.00133 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 1.35 20 99.7 0.068 11.3 4 116176 116176 3 20
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 1.35 1.45 99.3 0.415 3.1 3.7
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1u1v 1.35 19.73 110280 5844 99.71 0.12005 0.11844 0.1438 0.1503 0.1702 RANDOM 12.061
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 Key Refinement Restraint Deviation r_sphericity_free 10.385 r_dihedral_angle_1_deg 6.437 r_scangle_it 5.934 r_sphericity_bonded 4.349 r_scbond_it 4.225 r_mcangle_it 3.004 r_rigid_bond_restr 2.405 r_mcbond_it 2.258 r_angle_refined_deg 2.058 r_angle_other_deg 1.756
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 10.385 r_dihedral_angle_1_deg 6.437 r_scangle_it 5.934 r_sphericity_bonded 4.349 r_scbond_it 4.225 r_mcangle_it 3.004 r_rigid_bond_restr 2.405 r_mcbond_it 2.258 r_angle_refined_deg 2.058 r_angle_other_deg 1.756 r_symmetry_vdw_other 0.36 r_nbd_other 0.282 r_symmetry_hbond_refined 0.263 r_nbd_refined 0.254 r_symmetry_vdw_refined 0.225 r_xyhbond_nbd_refined 0.213 r_chiral_restr 0.149 r_nbtor_other 0.089 r_gen_planes_other 0.068 r_bond_other_d 0.067 r_gen_planes_refined 0.04 r_bond_refined_d 0.026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4248 Nucleic Acid Atoms Solvent Atoms 679 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XD data reduction XDS data scaling MOLREP phasing