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Crystal Structure of Phenazine Biosynthesis Protein PhzA/B from Burkholderia cepacia R18194, DHHA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B4O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 285 16-20% (w/v) PEG3350, 0.2 M NH4OAc, 0.1 M Bis-Tris pH 6.1-6.7; complex prepared by overnight soaking in mother liquor containing 50 mM DHHA, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.29 46.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.09 α = 90 b = 65.09 β = 90 c = 161.55 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 MARMOSAIC 225 mm CCD SI(111) monochromator 2008-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9809 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.65 20 100 0.066 0.139 16 14.1 48683 48675 3 33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.75 100 0.42 3.7 13.3 7754
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 apo structure THROUGHOUT 3B4O 1.65 19.81 46189 2447 99.99 0.15662 0.15469 0.1693 0.1939 0.2019 RANDOM 24.467
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_dihedral_angle_2_deg 36.323 r_dihedral_angle_4_deg 19.758 r_dihedral_angle_3_deg 14.549 r_dihedral_angle_1_deg 6.014 r_scangle_it 5.686 r_scbond_it 4 r_mcangle_it 2.457 r_angle_refined_deg 2.319 r_mcbond_it 2.205 r_angle_other_deg 1.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.323 r_dihedral_angle_4_deg 19.758 r_dihedral_angle_3_deg 14.549 r_dihedral_angle_1_deg 6.014 r_scangle_it 5.686 r_scbond_it 4 r_mcangle_it 2.457 r_angle_refined_deg 2.319 r_mcbond_it 2.205 r_angle_other_deg 1.103 r_mcbond_other 0.53 r_symmetry_vdw_refined 0.41 r_symmetry_hbond_refined 0.361 r_symmetry_vdw_other 0.342 r_nbd_refined 0.241 r_nbd_other 0.223 r_xyhbond_nbd_refined 0.222 r_nbtor_refined 0.19 r_chiral_restr 0.162 r_nbtor_other 0.089 r_bond_refined_d 0.031 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2619 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction XDS data reduction XSCALE data scaling