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BrvH, a flavin-dependent halogenase from Brevundimonas sp. BAL3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AQJ 2aqj, 2wet, 2oal, 5hy5 experimental model PDB 2WET 2aqj, 2wet, 2oal, 5hy5 experimental model PDB 2OAL 2aqj, 2wet, 2oal, 5hy5 experimental model PDB 5HY5 2aqj, 2wet, 2oal, 5hy5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277.15 0.95 M Na/K tartrate, 0.1 M MES pH 6
streak seeding
protein concentration 10 mg/ml
drop size 2 uL
drop ratio (protein:reservoir) 1:1
Crystal Properties Matthews coefficient Solvent content 2.45 49.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.62 α = 90 b = 88.35 β = 99.07 c = 70.11 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 4M 2017-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.96770 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 89.18 96.5 0.202 0.996 11.89 11.4 36507
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 98 1.422 0.661 1.84 11.2
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 2aqj, 2wet, 2oal, 5hy5 2.5 89.18 34697 1809 96.52 0.19687 0.19456 0.2024 0.24072 0.2468 RANDOM 39.358
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] -1.47 0.16 1.36 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.549 r_dihedral_angle_4_deg 18.526 r_dihedral_angle_3_deg 14.352 r_long_range_B_other 7.234 r_long_range_B_refined 7.233 r_dihedral_angle_1_deg 6.451 r_scangle_other 5.092 r_mcangle_it 4.689 r_mcangle_other 4.689 r_scbond_it 3.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.549 r_dihedral_angle_4_deg 18.526 r_dihedral_angle_3_deg 14.352 r_long_range_B_other 7.234 r_long_range_B_refined 7.233 r_dihedral_angle_1_deg 6.451 r_scangle_other 5.092 r_mcangle_it 4.689 r_mcangle_other 4.689 r_scbond_it 3.159 r_scbond_other 3.157 r_mcbond_it 2.969 r_mcbond_other 2.969 r_angle_refined_deg 1.572 r_angle_other_deg 0.998 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 7719 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing