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Crystal Structure of RebH, a FAD-dependent halogenase from Lechevalieria aerocolonigenes, the L-Tryptophan with FAD complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O9Z apo form of same protein in same lattice
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 Protein Solution (18 mg/ml protein, 0.050 M sodium chloride, 0.010 M TRIS pH 8.0)
mixed in a 1:1 ratio with the Well Solution
(0.9 M K2HPO4, 0.5 M NaH2PO4)
crystals soaked for 22 hours in solution of 0.6 M K2HPO4, 0.33 M NaH2PO4,
~0.005 M FAD, ~0.003 M L-tryptophan, 0.030 M NaCl,
Cryoprotected with: well solution supplemented with up to 30% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.5 64.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.492 α = 90 b = 114.492 β = 90 c = 231.935 γ = 120
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 300 mm CCD Adjustable focusing mirrors in K-B geometry 2006-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97931 APS 23-ID-D
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 2.15 49.576 98.8 0.102 24.905 20.4 92078
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 2.15 2.2 90.9 0.534 3.628 9.4 5634
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION 2O9Z THROUGHOUT apo form of same protein in same lattice 2.15 19.952 91914 4630 98.846 0.154 0.152 0.194 0.245 RANDOM 38.03
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] 0.031 0.015 0.031 -0.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.395 r_dihedral_angle_4_deg 15.397 r_dihedral_angle_3_deg 13.511 r_dihedral_angle_1_deg 6.171 r_scangle_it 3.39 r_scbond_it 2.086 r_angle_refined_deg 1.412 r_mcangle_it 1.157 r_mcbond_it 0.725 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.395 r_dihedral_angle_4_deg 15.397 r_dihedral_angle_3_deg 13.511 r_dihedral_angle_1_deg 6.171 r_scangle_it 3.39 r_scbond_it 2.086 r_angle_refined_deg 1.412 r_mcangle_it 1.157 r_mcbond_it 0.725 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.245 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.184 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8468 Nucleic Acid Atoms Solvent Atoms 1056 Heterogen Atoms 103
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction