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Co-crystal of pseudokinase DRIK1 (drought responsive inactive kinase 1) bound to ENMD-2076
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CPY PDB entry 6CPY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293.15 1 mM zinc chloride, 22% PEG6000, 100 mM MES, pH 6
Crystal Properties Matthews coefficient Solvent content 1.76 30.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.506 α = 90 b = 61.79 β = 90 c = 65.383 γ = 90
Symmetry Space Group P 21 2 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 PILATUS3 6M 2018-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.976230 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2 28.91 99.9 0.055 0.066 0.035 0.999 14.6 6.4 17144
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 100 0.871 1.025 0.537 0.723 2 6.8
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 PDB entry 6CPY 2 28.91 16362 753 99.88 0.20947 0.20741 0.2157 0.25136 0.2495 RANDOM 45.41
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] 0.37 -0.5 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.873 r_dihedral_angle_4_deg 16.71 r_dihedral_angle_3_deg 13.807 r_long_range_B_other 6.852 r_long_range_B_refined 6.851 r_dihedral_angle_1_deg 6.769 r_scangle_other 4.993 r_mcangle_it 4.266 r_mcangle_other 4.265 r_scbond_it 3.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.873 r_dihedral_angle_4_deg 16.71 r_dihedral_angle_3_deg 13.807 r_long_range_B_other 6.852 r_long_range_B_refined 6.851 r_dihedral_angle_1_deg 6.769 r_scangle_other 4.993 r_mcangle_it 4.266 r_mcangle_other 4.265 r_scbond_it 3.428 r_scbond_other 3.427 r_mcbond_it 3.072 r_mcbond_other 3.072 r_angle_refined_deg 1.141 r_angle_other_deg 0.888 r_chiral_restr 0.055 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1987 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing