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Crystal Structure of the Uba1-Ubiquitin Complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 298 L-proline, PEG 5000 MME, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.91 57.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.363 α = 90 b = 118.564 β = 90 c = 207.567 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 ADSC QUANTUM 315 2006-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.1000 NSLS X29A
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 2.7 50 98.5 0.115 7.7 6.5 77706
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 2.7 2.8 86.9 0.412 2.8
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 THROUGHOUT 2.7 20 73486 3899 98.45 0.19365 0.19077 0.1939 0.24687 0.1892 RANDOM 38.161
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] 0.35 0.74 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.155 r_dihedral_angle_4_deg 21.119 r_dihedral_angle_3_deg 19.808 r_dihedral_angle_1_deg 6.289 r_scangle_it 2.084 r_angle_refined_deg 1.366 r_scbond_it 1.228 r_mcangle_it 0.737 r_mcbond_it 0.413 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.155 r_dihedral_angle_4_deg 21.119 r_dihedral_angle_3_deg 19.808 r_dihedral_angle_1_deg 6.289 r_scangle_it 2.084 r_angle_refined_deg 1.366 r_scbond_it 1.228 r_mcangle_it 0.737 r_mcbond_it 0.413 r_nbtor_refined 0.311 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.213 r_xyhbond_nbd_refined 0.141 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.099 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17051 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 14
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection PHASER phasing