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Structure of a Ubiquitin like protein with an E1 fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IAA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.2M Potassium phosphate dibasic and 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.62 53.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.94 α = 90 b = 46.94 β = 90 c = 201.21 γ = 90
Symmetry Space Group P 43 2 2
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.918409 ESRF ID30B
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 2 50.3 100 0.096 10.1 16255
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
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 5iaa 2 50.3 15330 854 99.99 0.22212 0.22133 0.2247 0.23627 0.2464 RANDOM 41.956
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] 1.67 1.67 -3.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.713 r_dihedral_angle_4_deg 17.768 r_dihedral_angle_3_deg 14.002 r_long_range_B_refined 6.749 r_long_range_B_other 6.742 r_dihedral_angle_1_deg 6.189 r_scangle_other 5.087 r_mcangle_it 3.555 r_mcangle_other 3.553 r_scbond_it 3.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.713 r_dihedral_angle_4_deg 17.768 r_dihedral_angle_3_deg 14.002 r_long_range_B_refined 6.749 r_long_range_B_other 6.742 r_dihedral_angle_1_deg 6.189 r_scangle_other 5.087 r_mcangle_it 3.555 r_mcangle_other 3.553 r_scbond_it 3.285 r_scbond_other 3.283 r_mcbond_other 2.338 r_mcbond_it 2.337 r_angle_refined_deg 1.449 r_angle_other_deg 1.22 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.005 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 1394 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing