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Structure of RIP2K(D146N) with bound Staurosporine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NG0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 .1 M MES pH6.5, 2M NaCl, 0.1 mM Na(H2PO4), 0.1 mM of K(H2PO4)
Crystal Properties Matthews coefficient Solvent content 3.35 63.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.083 α = 90 b = 96.083 β = 90 c = 202.266 γ = 90
Symmetry Space Group P 41 21 2
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 PILATUS3 6M 2015-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.972 ESRF ID29
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 2.8 48.04 99.9 0.192 8.8 7.2 22957
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 5NG0 2.8 20.85 22957 1153 99.87 0.20931 0.20846 0.2098 0.22562 0.2253 RANDOM 56.431
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] 2.13 2.13 -4.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.922 r_dihedral_angle_3_deg 16.314 r_dihedral_angle_4_deg 9.936 r_long_range_B_refined 7.322 r_dihedral_angle_1_deg 5.465 r_mcangle_it 3.981 r_mcbond_it 2.213 r_scbond_it 2.109 r_angle_refined_deg 1.732 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.922 r_dihedral_angle_3_deg 16.314 r_dihedral_angle_4_deg 9.936 r_long_range_B_refined 7.322 r_dihedral_angle_1_deg 5.465 r_mcangle_it 3.981 r_mcbond_it 2.213 r_scbond_it 2.109 r_angle_refined_deg 1.732 r_chiral_restr 0.089 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4506 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing