☰ Navigation Tabs
Crystal structure of WT Trm5b from Pyrococcus abyssi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HJM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 12% (w/v) PEG 3350, 100 mM HEPES (pH 7.5), 100 mM Ca(OAc)2 and 100 mM KCl
Crystal Properties Matthews coefficient Solvent content 2.3 46.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.444 α = 90 b = 88.567 β = 90 c = 95.164 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 CCD OXFORD ONYX CCD 2017-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE Agilent SuperNova 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.3 25.15 99.6 0.204 6.3 4.1 5639
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.48 100 0.98 4.2
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 5HJM 3.3 25.15 5338 279 99.36 0.24386 0.24158 0.2449 0.28847 0.2824 RANDOM 67.721
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] -1.87 -3.75 5.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.095 r_dihedral_angle_3_deg 18.321 r_dihedral_angle_4_deg 11.313 r_long_range_B_other 10.326 r_long_range_B_refined 10.323 r_scangle_other 7.228 r_mcangle_it 7.187 r_mcangle_other 7.185 r_dihedral_angle_1_deg 6.284 r_mcbond_other 4.486
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.095 r_dihedral_angle_3_deg 18.321 r_dihedral_angle_4_deg 11.313 r_long_range_B_other 10.326 r_long_range_B_refined 10.323 r_scangle_other 7.228 r_mcangle_it 7.187 r_mcangle_other 7.185 r_dihedral_angle_1_deg 6.284 r_mcbond_other 4.486 r_mcbond_it 4.485 r_scbond_it 4.427 r_scbond_other 4.427 r_angle_refined_deg 1.269 r_angle_other_deg 0.984 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_bond_other_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 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 2390 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction SCALA data scaling PHASER phasing