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Human Ubiquitin-activating Enzyme 5 in Complex with AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZFN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.2 287 1 M LITHIUM SULPHATE, 0.3 M AMMONIUM SULPHATE,0.1 M SODIUM CITRATE, PH 6.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 287K
Crystal Properties Matthews coefficient Solvent content 2.51 51.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.394 α = 90 b = 77.394 β = 90 c = 205.892 γ = 120
Symmetry Space Group P 32 2 1
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 2009-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 50 100 0.131 23.878 10.5 34922 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.25 2.29 100 0.838 2.89 8.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1ZFN 2.25 40.82 34835 33065 1770 99.97 0.20562 0.20303 0.2167 0.25485 0.2598 RANDOM 55.853
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] 0.96 0.48 0.96 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.302 r_dihedral_angle_4_deg 25.116 r_dihedral_angle_3_deg 18.224 r_dihedral_angle_1_deg 5.594 r_scangle_it 4.252 r_scbond_it 3.262 r_mcangle_it 1.967 r_angle_refined_deg 1.531 r_mcbond_it 1.157 r_chiral_restr 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.302 r_dihedral_angle_4_deg 25.116 r_dihedral_angle_3_deg 18.224 r_dihedral_angle_1_deg 5.594 r_scangle_it 4.252 r_scbond_it 3.262 r_mcangle_it 1.967 r_angle_refined_deg 1.531 r_mcbond_it 1.157 r_chiral_restr 0.12 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3525 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 29
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling