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Structure of phenazine antibiotic biosynthesis protein with substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HGU pdb entry 3HGU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 Na/K Phosphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.67 66.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.129 α = 90 b = 193.129 β = 90 c = 193.129 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 IMAGE PLATE RIGAKU RAXIS IV++ 2008-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.8 48.28 0.1 12 14.7 29538
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 2.8 2.9 0.5 3.2 12.6 2930
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 3HGU 2.8 26.78 27888 1495 99.89 0.21635 0.21207 0.2131 0.2881 0.287 RANDOM 36.45
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 35.864 r_dihedral_angle_4_deg 23.68 r_dihedral_angle_3_deg 22.246 r_dihedral_angle_1_deg 9.767 r_scangle_it 4.32 r_angle_refined_deg 2.713 r_scbond_it 2.697 r_mcangle_it 1.787 r_mcbond_it 1.015 r_nbtor_refined 0.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.864 r_dihedral_angle_4_deg 23.68 r_dihedral_angle_3_deg 22.246 r_dihedral_angle_1_deg 9.767 r_scangle_it 4.32 r_angle_refined_deg 2.713 r_scbond_it 2.697 r_mcangle_it 1.787 r_mcbond_it 1.015 r_nbtor_refined 0.349 r_nbd_refined 0.294 r_symmetry_vdw_refined 0.235 r_xyhbond_nbd_refined 0.196 r_symmetry_hbond_refined 0.191 r_chiral_restr 0.176 r_bond_refined_d 0.03 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5538 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 40
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling