☰ Navigation Tabs
Free serine kinase (E30Q mutant) in complex with phosphoserine and AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5X0E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.7 293 PEG 3350, serine
Crystal Properties Matthews coefficient Solvent content 2.21 44.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.824 α = 90 b = 43.4 β = 90 c = 157.545 γ = 90
Symmetry Space Group P 21 21 21
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 1.43 50 97.5 21.7 6.2 45510
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 5X0E 1.43 50 43174 2275 97.43 0.18134 0.18045 0.19827 0.2417 RANDOM 16.253
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] -0.45 0.35 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.238 r_dihedral_angle_3_deg 11.259 r_dihedral_angle_4_deg 10.86 r_dihedral_angle_1_deg 6.097 r_long_range_B_refined 3.287 r_long_range_B_other 3.051 r_angle_refined_deg 1.369 r_angle_other_deg 0.861 r_scangle_other 0.827 r_mcangle_it 0.655
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.238 r_dihedral_angle_3_deg 11.259 r_dihedral_angle_4_deg 10.86 r_dihedral_angle_1_deg 6.097 r_long_range_B_refined 3.287 r_long_range_B_other 3.051 r_angle_refined_deg 1.369 r_angle_other_deg 0.861 r_scangle_other 0.827 r_mcangle_it 0.655 r_mcangle_other 0.654 r_scbond_other 0.509 r_scbond_it 0.508 r_mcbond_it 0.377 r_mcbond_other 0.377 r_chiral_restr 0.081 r_bond_refined_d 0.007 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 1906 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling REFMAC phasing