☰ Navigation Tabs
Structure of the Cif:Nedd8 complex - Photorhabdus luminescens Cycle Inhibiting Factor in complex with human Nedd8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GQJ PDB ENTRIES 3GQJ and 1NDD experimental model PDB 1NDD PDB ENTRIES 3GQJ and 1NDD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.7 289 20% PEG 4000, 200mM sodium acetate, 100mM MES pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.89 34.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.73 α = 90 b = 56.09 β = 104.13 c = 67.55 γ = 90
Symmetry Space Group P 1 21 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 315r 2011-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.91340 Diamond I02
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 1.6 42.6 96.4 0.052 11.5 4.4 39093 39093 1 1
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) 1 1.6 1.69 96.2 0.288 3 4.3
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 PDB ENTRIES 3GQJ and 1NDD 1.6 38.2 39093 35599 1881 95.87 0.16848 0.16485 0.1632 0.23624 0.2355 RANDOM 23.474
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] 0.21 -0.43 -0.46 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.814 r_dihedral_angle_4_deg 16.983 r_dihedral_angle_3_deg 14.651 r_scangle_it 7.642 r_dihedral_angle_1_deg 6.873 r_scbond_it 5.333 r_mcangle_it 3.628 r_rigid_bond_restr 2.829 r_mcbond_it 2.413 r_angle_refined_deg 2.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.814 r_dihedral_angle_4_deg 16.983 r_dihedral_angle_3_deg 14.651 r_scangle_it 7.642 r_dihedral_angle_1_deg 6.873 r_scbond_it 5.333 r_mcangle_it 3.628 r_rigid_bond_restr 2.829 r_mcbond_it 2.413 r_angle_refined_deg 2.047 r_chiral_restr 0.143 r_bond_refined_d 0.024 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2586 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 1
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling