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Biophysical and structural characterization of the thermostable WD40 domain of a prokaryotic protein, Thermomonospora curvata PkwA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, and 2.0 M Ammonium sulfate with additive from Hampton Research Silver Bullet additive Kit.
Crystal Properties Matthews coefficient Solvent content 3.17 61.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.687 α = 78.77 b = 107.257 β = 89.33 c = 110.267 γ = 88.91
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 MARRESEARCH 2016-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 1.0000 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 50 93.2 11.33 2.9 62971
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54
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 (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 2.6 50.01 51766 2665 90.11 0.22645 0.22474 0.2301 0.25912 0.2588 RANDOM 41.446
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] 0.85 0.6 -0.15 -0.56 -1.36 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.151 r_dihedral_angle_4_deg 23.329 r_dihedral_angle_3_deg 19.344 r_long_range_B_refined 12.526 r_long_range_B_other 12.522 r_scangle_other 8.994 r_dihedral_angle_1_deg 6.122 r_scbond_it 5.906 r_scbond_other 5.906 r_mcangle_it 5.422
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.151 r_dihedral_angle_4_deg 23.329 r_dihedral_angle_3_deg 19.344 r_long_range_B_refined 12.526 r_long_range_B_other 12.522 r_scangle_other 8.994 r_dihedral_angle_1_deg 6.122 r_scbond_it 5.906 r_scbond_other 5.906 r_mcangle_it 5.422 r_mcangle_other 5.422 r_mcbond_it 3.485 r_mcbond_other 3.484 r_angle_other_deg 3.319 r_angle_refined_deg 2.126 r_chiral_restr 0.125 r_bond_refined_d 0.024 r_gen_planes_other 0.013 r_bond_other_d 0.012 r_gen_planes_refined 0.01 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 10697 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing