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Crystal Structure of Pathogenesis-related Protein 1G (PR-1G) Kinase Domain from Cacao
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UIM PDB entry 3UIM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 18% PEG8000, 0.2 M magnesium acetate, 0.1 M SSB buffer
Crystal Properties Matthews coefficient Solvent content 2.4 48.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.798 α = 90 b = 56.798 β = 90 c = 358.04 γ = 120
Symmetry Space Group P 61 2 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 PILATUS 6M-F 2017-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979100 APS 24-ID-C
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 1.7 30 100 0.081 0.086 0.02 0.999 17.4 18.6 39498
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 99.9 1.73 0.544 0.829 1.4 18.8
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 3UIM 1.7 30 37364 1977 99.94 0.2098 0.20835 0.219 0.23846 0.2446 RANDOM 41.402
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] 0.52 0.26 0.52 -1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.943 r_dihedral_angle_4_deg 24.89 r_dihedral_angle_3_deg 14.059 r_dihedral_angle_1_deg 5.954 r_long_range_B_refined 5.899 r_long_range_B_other 5.856 r_scangle_other 2.666 r_mcangle_it 2.37 r_mcangle_other 2.37 r_angle_refined_deg 1.629
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.943 r_dihedral_angle_4_deg 24.89 r_dihedral_angle_3_deg 14.059 r_dihedral_angle_1_deg 5.954 r_long_range_B_refined 5.899 r_long_range_B_other 5.856 r_scangle_other 2.666 r_mcangle_it 2.37 r_mcangle_other 2.37 r_angle_refined_deg 1.629 r_scbond_it 1.619 r_scbond_other 1.619 r_mcbond_it 1.406 r_mcbond_other 1.403 r_angle_other_deg 1.013 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 2255 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing