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Trp-7-Hal - Consensus designed artificial tryptophan-7-halogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Lithium citrate tribasic tetrahydrate, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.61 52.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.103 α = 102.274 b = 106.497 β = 90.821 c = 110.639 γ = 101.352
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2023-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.5 54.02 98.7 0.136 0.16 0.084 0.99 6.6 3.6 85116
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.55 98 0.878 1.028 0.532 0.697 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.5 54.02 85111 4154 98.7 0.222 0.2201 0.2246 0.2593 0.2626 RANDOM 41.976
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] 4.055 -2.123 0.9 -0.265 -1.158 -2.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.374 r_dihedral_angle_3_deg 13.588 r_dihedral_angle_2_deg 10.424 r_lrange_it 9.212 r_lrange_other 9.212 r_scangle_it 7.168 r_scangle_other 7.168 r_dihedral_angle_1_deg 6.75 r_mcangle_it 5.725 r_mcangle_other 5.725
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.374 r_dihedral_angle_3_deg 13.588 r_dihedral_angle_2_deg 10.424 r_lrange_it 9.212 r_lrange_other 9.212 r_scangle_it 7.168 r_scangle_other 7.168 r_dihedral_angle_1_deg 6.75 r_mcangle_it 5.725 r_mcangle_other 5.725 r_scbond_it 4.626 r_scbond_other 4.626 r_mcbond_it 3.812 r_mcbond_other 3.812 r_angle_refined_deg 1.586 r_angle_other_deg 0.567 r_symmetry_xyhbond_nbd_refined 0.357 r_nbd_refined 0.221 r_symmetry_nbd_refined 0.215 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.186 r_nbd_other 0.169 r_xyhbond_nbd_refined 0.16 r_symmetry_xyhbond_nbd_other 0.09 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.077 r_ncsr_local_group_6 0.063 r_ncsr_local_group_5 0.052 r_ncsr_local_group_3 0.05 r_ncsr_local_group_2 0.049 r_ncsr_local_group_4 0.046 r_ncsr_local_group_1 0.045 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16837 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing PDB_EXTRACT data extraction