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Crystal structure of halogenase PltM in complex with partially bound FAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BZN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 294 0.1 M Tris pH 8, 0.2 M NaCl, 0.1 M CaCl2 and 12-17% PEG 8000, soaked in same with 0.5 mM FAD
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.815 α = 90 b = 157.234 β = 90 c = 214.008 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX300-HS 2017-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 2.05 50 98.2 0.175 18.1 7.5 132527 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 93.9 0.8 0.786 7.1
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 6BZN 2.05 40 125848 6596 97.69 0.22025 0.21892 0.2243 0.24549 0.2499 RANDOM 21.512
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] 0.04 -0.05 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.42 r_dihedral_angle_3_deg 15.023 r_dihedral_angle_4_deg 13.617 r_dihedral_angle_1_deg 5.92 r_angle_other_deg 3.704 r_long_range_B_refined 2.203 r_long_range_B_other 2.144 r_angle_refined_deg 1.207 r_mcangle_it 1.121 r_mcangle_other 1.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.42 r_dihedral_angle_3_deg 15.023 r_dihedral_angle_4_deg 13.617 r_dihedral_angle_1_deg 5.92 r_angle_other_deg 3.704 r_long_range_B_refined 2.203 r_long_range_B_other 2.144 r_angle_refined_deg 1.207 r_mcangle_it 1.121 r_mcangle_other 1.121 r_scangle_other 0.912 r_mcbond_it 0.606 r_mcbond_other 0.605 r_scbond_it 0.481 r_scbond_other 0.481 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15791 Nucleic Acid Atoms Solvent Atoms 455 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing