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Caldiarchaeum Subterraneum Ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 100 mM sodium acetate pH 4.5, 200 mM lithium sulfate, 50% PEG 400
Crystal Properties Matthews coefficient Solvent content 1.94 36.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.45 α = 90 b = 42.8 β = 90 c = 51.41 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-F 2014-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 SLS X10SA
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 1.05 32.9 98.2 0.051 0.999 22.39 11 30589
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 1.05 1.11 89 0.627 0.862 2.18 5.1
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) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1UBQ 1.05 32.89 29058 1530 98.22 0.15544 0.1534 0.157 0.19512 0.1836 RANDOM 15.22
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] 0.03 -0.37 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.238 r_sphericity_free 29.21 r_dihedral_angle_4_deg 20.89 r_dihedral_angle_3_deg 13.561 r_sphericity_bonded 10.02 r_dihedral_angle_1_deg 7.689 r_rigid_bond_restr 4.489 r_long_range_B_refined 3.465 r_long_range_B_other 3.368 r_scangle_other 2.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.238 r_sphericity_free 29.21 r_dihedral_angle_4_deg 20.89 r_dihedral_angle_3_deg 13.561 r_sphericity_bonded 10.02 r_dihedral_angle_1_deg 7.689 r_rigid_bond_restr 4.489 r_long_range_B_refined 3.465 r_long_range_B_other 3.368 r_scangle_other 2.96 r_scbond_it 2.63 r_scbond_other 2.612 r_angle_refined_deg 2.337 r_mcangle_other 2.02 r_mcangle_it 2.006 r_mcbond_it 1.627 r_mcbond_other 1.571 r_angle_other_deg 0.907 r_chiral_restr 0.13 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 569 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing