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Structure of human PKCBeta Kinase domain with Ruboxistaurin, D427N mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PFQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.17 293 0.1M Citrate pH 5.17
12.3% PEG 6k
Crystal Properties Matthews coefficient Solvent content 3.45 64.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.327 α = 90 b = 102.327 β = 90 c = 82.827 γ = 120
Symmetry Space Group P 31 2 1
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 EIGER2 XE CdTe 9M 2022-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.67 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.42 60.511 100 0.995 3.8 20 7021
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.42 3.47 0.175 0.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.425 60.511 7006 364 99.829 0.218 0.2142 0.2146 0.2897 0.2909 144.059
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] -0.507 -0.253 -0.507 1.644
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 23.781 r_lrange_other 23.78 r_dihedral_angle_2_deg 23.658 r_dihedral_angle_3_deg 19.657 r_scangle_it 18.913 r_scangle_other 18.908 r_mcangle_it 16.524 r_mcangle_other 16.519 r_dihedral_angle_6_deg 16.006 r_scbond_it 12.54
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 23.781 r_lrange_other 23.78 r_dihedral_angle_2_deg 23.658 r_dihedral_angle_3_deg 19.657 r_scangle_it 18.913 r_scangle_other 18.908 r_mcangle_it 16.524 r_mcangle_other 16.519 r_dihedral_angle_6_deg 16.006 r_scbond_it 12.54 r_scbond_other 12.535 r_mcbond_it 10.809 r_mcbond_other 10.8 r_dihedral_angle_1_deg 7.458 r_angle_refined_deg 2.193 r_angle_other_deg 1.059 r_nbd_refined 0.192 r_nbtor_refined 0.169 r_symmetry_nbd_refined 0.163 r_symmetry_nbd_other 0.139 r_chiral_restr 0.105 r_xyhbond_nbd_refined 0.101 r_nbd_other 0.1 r_symmetry_nbtor_other 0.07 r_symmetry_xyhbond_nbd_refined 0.042 r_gen_planes_refined 0.012 r_bond_refined_d 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2529 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement DIALS data reduction gemmi data extraction DIALS data scaling MrBUMP phasing PHASER phasing