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DIHYDROOROTASE FROM AQUIFEX AEOLICUS UNDER 1200 BAR OF HYDROSTATIC PRESSURE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XRF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 ETHANOL (12%), PEG 400 (4%), ACETATE BUFFER (0.1M). PROTEIN 6 MG/ML
Crystal Properties Matthews coefficient Solvent content 3.17 61.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.651 α = 90 b = 176.148 β = 90 c = 65.676 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD MARRESEARCH 2016-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID27 0.3738 ESRF ID27
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 45.33 99.6 0.157 0.062 0.995 8.8 7.1 20901 49.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 99 1.17 0.46 1.9 7.1
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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS NONE 1XRF 2.6 40.3 16487 99.33 0.15063 0.15063 0.1595 54.645
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] 0.05 -0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.947 r_dihedral_angle_4_deg 24.482 r_dihedral_angle_3_deg 19.99 r_long_range_B_refined 10.971 r_long_range_B_other 10.963 r_scangle_other 9 r_dihedral_angle_1_deg 8.343 r_mcangle_it 6.601 r_mcangle_other 6.599 r_scbond_it 6.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.947 r_dihedral_angle_4_deg 24.482 r_dihedral_angle_3_deg 19.99 r_long_range_B_refined 10.971 r_long_range_B_other 10.963 r_scangle_other 9 r_dihedral_angle_1_deg 8.343 r_mcangle_it 6.601 r_mcangle_other 6.599 r_scbond_it 6.134 r_scbond_other 6.131 r_mcbond_it 4.77 r_mcbond_other 4.738 r_angle_refined_deg 1.237 r_angle_other_deg 0.396 r_chiral_restr 0.061 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 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 2889 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing