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Free serine kinase (E30A mutant) in complex with AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5X0B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.9 293 PEG 3350, serine
Crystal Properties Matthews coefficient Solvent content 2.23 44.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.903 α = 90 b = 70.032 β = 90 c = 88.381 γ = 90
Symmetry Space Group P 21 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 EIGER X 4M 2015-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.100 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.76 50 97.7 13.4 5.3 24624
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5X0B 1.76 50 23360 1240 97.55 0.22496 0.22301 0.26097 0.2714 RANDOM 26.784
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] -0.57 -0.41 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.938 r_dihedral_angle_3_deg 12.522 r_dihedral_angle_4_deg 12.506 r_dihedral_angle_1_deg 7.025 r_long_range_B_refined 3.843 r_long_range_B_other 3.775 r_angle_refined_deg 1.541 r_angle_other_deg 0.917 r_scangle_other 0.438 r_mcangle_it 0.392
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.938 r_dihedral_angle_3_deg 12.522 r_dihedral_angle_4_deg 12.506 r_dihedral_angle_1_deg 7.025 r_long_range_B_refined 3.843 r_long_range_B_other 3.775 r_angle_refined_deg 1.541 r_angle_other_deg 0.917 r_scangle_other 0.438 r_mcangle_it 0.392 r_mcangle_other 0.392 r_scbond_it 0.267 r_scbond_other 0.267 r_mcbond_it 0.218 r_mcbond_other 0.218 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1839 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling REFMAC phasing