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Crystal structure of tryptophan 5-halogenase (PyrH) complex with substrate tryptophan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AQJ PDB ENTRY 2AQJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.2 0.05M SODIUM CACODYLATE BUFFER PH6.2, 1.4M LI2SO4 0.01M MGCL2
Crystal Properties Matthews coefficient Solvent content 2.75 55.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.7 α = 90 b = 141.08 β = 90 c = 122.95 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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.7 100 98.6 0.08 12.6 4.7 228784 2
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 1.7 1.9 98.7 0.22 4.3 4.8
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 2AQJ 1.7 100.5 228784 12099 88.5 0.216 0.215 0.224 0.248 0.2577 RANDOM 12.56
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] -0.03 0.87 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.2 r_dihedral_angle_4_deg 18.604 r_dihedral_angle_3_deg 12.347 r_dihedral_angle_1_deg 5.946 r_scangle_it 3.064 r_scbond_it 1.913 r_angle_refined_deg 1.289 r_mcangle_it 1.139 r_angle_other_deg 0.925 r_mcbond_it 0.636
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.2 r_dihedral_angle_4_deg 18.604 r_dihedral_angle_3_deg 12.347 r_dihedral_angle_1_deg 5.946 r_scangle_it 3.064 r_scbond_it 1.913 r_angle_refined_deg 1.289 r_mcangle_it 1.139 r_angle_other_deg 0.925 r_mcbond_it 0.636 r_mcbond_other 0.21 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15984 Nucleic Acid Atoms Solvent Atoms 1452 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing