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Free serine kinase (E30A mutant) in complex with ADP
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 8.5 293 PEG 3350, POPSO
Crystal Properties Matthews coefficient Solvent content 2.18 43.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.766 α = 90 b = 69.745 β = 90 c = 87.159 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 95 CCD ADSC QUANTUM 315r 2016-02-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 1.9 50 99.9 12.4 7 19825
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 1.9 50 18800 999 99.83 0.25349 0.25257 0.27046 0.2899 RANDOM 31.761
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] -0.27 0.76 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.435 r_dihedral_angle_3_deg 12.994 r_dihedral_angle_4_deg 11.684 r_dihedral_angle_1_deg 6.643 r_long_range_B_refined 3.482 r_long_range_B_other 3.426 r_angle_refined_deg 1.399 r_angle_other_deg 0.859 r_scangle_other 0.248 r_scbond_it 0.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.435 r_dihedral_angle_3_deg 12.994 r_dihedral_angle_4_deg 11.684 r_dihedral_angle_1_deg 6.643 r_long_range_B_refined 3.482 r_long_range_B_other 3.426 r_angle_refined_deg 1.399 r_angle_other_deg 0.859 r_scangle_other 0.248 r_scbond_it 0.152 r_scbond_other 0.152 r_mcangle_it 0.097 r_mcangle_other 0.097 r_chiral_restr 0.072 r_mcbond_it 0.054 r_mcbond_other 0.054 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 1755 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling REFMAC phasing