☰ Navigation Tabs
Rhodococcus jostii RHA1 thiamine diphosphate-dependent 4-hydroxybenzoylformate decarboxylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QSI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 300 0.16 M ammonium sulfate, 20% PEG8000, 0.1 mM Mes pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.57 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.5 α = 90 b = 132.24 β = 90 c = 138.7 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 PIXEL DECTRIS PILATUS 6M 2017-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97948 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.6 123.5 100 0.154 0.997 11.5 10 70459 -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 2.6 2.74 100 2.187 0.461 10.2
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6QSI 2.6 90.423 70459 2975 99.99 0.196 0.1963 0.1946 0.2329 0.2246 81.639
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] 5.019 -3.673 -1.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.876 r_dihedral_angle_3_deg 18.527 r_dihedral_angle_4_deg 18.073 r_lrange_other 8.051 r_lrange_it 8.05 r_dihedral_angle_1_deg 7.853 r_scangle_it 4.288 r_scangle_other 4.288 r_mcangle_it 4.016 r_mcangle_other 4.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.876 r_dihedral_angle_3_deg 18.527 r_dihedral_angle_4_deg 18.073 r_lrange_other 8.051 r_lrange_it 8.05 r_dihedral_angle_1_deg 7.853 r_scangle_it 4.288 r_scangle_other 4.288 r_mcangle_it 4.016 r_mcangle_other 4.016 r_scbond_it 2.702 r_scbond_other 2.678 r_mcbond_it 2.432 r_mcbond_other 2.432 r_angle_refined_deg 1.803 r_angle_other_deg 1.339 r_metal_ion_refined 0.298 r_nbd_other 0.254 r_symmetry_nbd_refined 0.248 r_nbd_refined 0.218 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.133 r_symmetry_xyhbond_nbd_refined 0.129 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.075 r_ncsr_local_group_1 0.042 r_ncsr_local_group_4 0.041 r_ncsr_local_group_5 0.038 r_ncsr_local_group_2 0.037 r_ncsr_local_group_6 0.037 r_ncsr_local_group_3 0.035 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15556 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing