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Structure of RIP2K(L294F) with bound AMPPCP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FB8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Hepes 100 mM pH 7.5, 1 mM MgCl2, 2.0 M LiCl and 5% PEG 6000
Crystal Properties Matthews coefficient Solvent content 3.2 61.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.18 α = 90 b = 94.18 β = 90 c = 201.25 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 2013-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976 ESRF ID23-1
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 47.25 92.8 0.035 19.9 3.8 54007
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 2FB8 2 20 54007 2886 91.78 0.17134 0.17028 0.172 0.19143 0.1732 RANDOM 37.919
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] 1.4 1.4 -2.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.604 r_dihedral_angle_4_deg 19.704 r_dihedral_angle_3_deg 13.517 r_long_range_B_refined 6.926 r_dihedral_angle_1_deg 5.653 r_mcangle_it 3.491 r_scbond_it 2.878 r_mcbond_it 2.192 r_angle_refined_deg 1.338 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.604 r_dihedral_angle_4_deg 19.704 r_dihedral_angle_3_deg 13.517 r_long_range_B_refined 6.926 r_dihedral_angle_1_deg 5.653 r_mcangle_it 3.491 r_scbond_it 2.878 r_mcbond_it 2.192 r_angle_refined_deg 1.338 r_chiral_restr 0.09 r_bond_refined_d 0.04 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_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 4481 Nucleic Acid Atoms Solvent Atoms 397 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing