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ParkinK211N in complex with phospho NEDD8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8IKV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 0.1 M, MMT, 7.0, 25% w/v, PEG 1500
Crystal Properties Matthews coefficient Solvent content 2 38.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.249 α = 90 b = 74.603 β = 90 c = 80.067 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 PIXEL DECTRIS EIGER X 9M 2023-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8731 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.8 39.86 99.17 0.996 10.25 4.5 32755
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.864 0.826
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 8IKV 1.8 39.86 32755 1753 99.188 0.181 0.1788 0.1802 0.2116 0.2136 22.367
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] -0.169 -0.357 0.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.247 r_dihedral_angle_4_deg 15.816 r_dihedral_angle_3_deg 14.81 r_lrange_it 7.597 r_dihedral_angle_1_deg 6.492 r_scangle_it 3.477 r_scbond_it 2.212 r_mcangle_it 2.092 r_angle_refined_deg 1.479 r_mcbond_it 1.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.247 r_dihedral_angle_4_deg 15.816 r_dihedral_angle_3_deg 14.81 r_lrange_it 7.597 r_dihedral_angle_1_deg 6.492 r_scangle_it 3.477 r_scbond_it 2.212 r_mcangle_it 2.092 r_angle_refined_deg 1.479 r_mcbond_it 1.349 r_nbtor_refined 0.311 r_symmetry_xyhbond_nbd_refined 0.203 r_nbd_refined 0.202 r_symmetry_nbd_refined 0.191 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.095 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2991 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing