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Structure of apo GRMZM2G135359 pseudokinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UV4 PDB entry 5UV4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.15 M potassium bromide, 30% PEG2000 MME
Crystal Properties Matthews coefficient Solvent content 1.97 37.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.492 α = 90 b = 61.496 β = 90 c = 144.764 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 16M 2017-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.7 19.82 99.9 0.064 0.07 0.029 16.4 10.88 61213
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 1.7 1.73 99.9 2.035 2.247 0.943 0.519
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 5UV4 1.7 19.82 58167 2974 99.82 0.20021 0.1994 0.2085 0.21529 0.2195 RANDOM 34.262
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] -1.23 -1.32 2.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.948 r_dihedral_angle_4_deg 17.95 r_dihedral_angle_3_deg 11.92 r_dihedral_angle_1_deg 5.293 r_long_range_B_refined 4.645 r_long_range_B_other 4.626 r_scangle_other 3.299 r_mcangle_other 2.671 r_mcangle_it 2.67 r_scbond_it 2.037
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.948 r_dihedral_angle_4_deg 17.95 r_dihedral_angle_3_deg 11.92 r_dihedral_angle_1_deg 5.293 r_long_range_B_refined 4.645 r_long_range_B_other 4.626 r_scangle_other 3.299 r_mcangle_other 2.671 r_mcangle_it 2.67 r_scbond_it 2.037 r_scbond_other 2.037 r_mcbond_it 1.671 r_mcbond_other 1.664 r_angle_refined_deg 1.102 r_angle_other_deg 0.737 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 4204 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing