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Free serine kinase (E30Q 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 9 293 PEG 3350, serine
Crystal Properties Matthews coefficient Solvent content 2.19 43.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.936 α = 90 b = 69.602 β = 90 c = 87.431 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 CCD RAYONIX MX225HE 2016-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000 SPring-8 BL38B1
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 1.65 50 99 20.9 7 29948
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 FOURIER SYNTHESIS THROUGHOUT 5X0B 1.65 50 28412 1504 99.8 0.23373 0.23247 0.2393 0.257 0.2652 RANDOM 28.517
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 -0.49 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.232 r_dihedral_angle_3_deg 12.2 r_dihedral_angle_4_deg 9.741 r_dihedral_angle_1_deg 7.263 r_long_range_B_refined 4.123 r_long_range_B_other 4.06 r_angle_refined_deg 1.59 r_angle_other_deg 0.941 r_scangle_other 0.737 r_mcangle_it 0.644
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.232 r_dihedral_angle_3_deg 12.2 r_dihedral_angle_4_deg 9.741 r_dihedral_angle_1_deg 7.263 r_long_range_B_refined 4.123 r_long_range_B_other 4.06 r_angle_refined_deg 1.59 r_angle_other_deg 0.941 r_scangle_other 0.737 r_mcangle_it 0.644 r_mcangle_other 0.643 r_scbond_it 0.459 r_scbond_other 0.459 r_mcbond_it 0.368 r_mcbond_other 0.368 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.003 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 1793 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling REFMAC phasing