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crystal structure of linear di-ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ PDB ENTRY 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 22% PEG 3350 AND 200 MM ZNOAC, pH 7
Crystal Properties Matthews coefficient Solvent content 2.8 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.572 α = 90 b = 105.572 β = 90 c = 105.572 γ = 90
Symmetry Space Group P 43 3 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 CCD ADSC CCD 2007-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.25 74.74 99.1 0.11 27.4 17.1 9985 2
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 2.25 2.37 96.9 0.54 2 5.8
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 PDB ENTRY 1UBQ 2.25 30 9431 478 98.7 0.26 0.259 0.2625 0.276 0.2823 RANDOM 77.15
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.869 r_dihedral_angle_4_deg 24.087 r_dihedral_angle_3_deg 19.553 r_dihedral_angle_1_deg 7.51 r_scangle_it 3.94 r_scbond_it 2.518 r_angle_refined_deg 1.927 r_mcangle_it 1.441 r_mcbond_it 0.895 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.869 r_dihedral_angle_4_deg 24.087 r_dihedral_angle_3_deg 19.553 r_dihedral_angle_1_deg 7.51 r_scangle_it 3.94 r_scbond_it 2.518 r_angle_refined_deg 1.927 r_mcangle_it 1.441 r_mcbond_it 0.895 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.261 r_nbd_refined 0.226 r_symmetry_hbond_refined 0.214 r_xyhbond_nbd_refined 0.183 r_chiral_restr 0.12 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1185 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing