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Structure of NEDD8-activating enzyme in complex with NEDD8 and MLN4924
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R4M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 293 1.8 M tri-ammonium citrate pH 7.0, 4% (v/v) 1,3 butanediol, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.62 66.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.03 α = 90 b = 228.715 β = 90 c = 229.307 γ = 90
Symmetry Space Group I 2 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 93 CCD MAR CCD 165 mm 2008-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97929 APS 31-ID
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 3 49.36 92.3 0.094 15.9 5.9
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 1R4M 3 49.36 66102 3515 97.87 0.23325 0.23046 0.2275 0.28702 0.283 RANDOM 66.768
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] 6.91 -3.48 -3.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.568 r_dihedral_angle_3_deg 17.111 r_dihedral_angle_4_deg 15.884 r_dihedral_angle_1_deg 5.662 r_scangle_it 1.445 r_angle_refined_deg 1.147 r_mcangle_it 1.086 r_scbond_it 0.871 r_mcbond_it 0.577 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.568 r_dihedral_angle_3_deg 17.111 r_dihedral_angle_4_deg 15.884 r_dihedral_angle_1_deg 5.662 r_scangle_it 1.445 r_angle_refined_deg 1.147 r_mcangle_it 1.086 r_scbond_it 0.871 r_mcbond_it 0.577 r_nbtor_refined 0.308 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.126 r_chiral_restr 0.08 r_bond_refined_d 0.008 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 15986 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement