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Free serine kinase in complex with AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VK1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 PEG 3350, serine
Crystal Properties Matthews coefficient Solvent content 2.2 44.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.052 α = 90 b = 69.866 β = 90 c = 87.417 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 2015-10-06 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 1.75 50 99.8 16.9 6.7 25375
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 MOLECULAR REPLACEMENT THROUGHOUT 1VK1 1.75 50 24069 1280 99.74 0.22963 0.22848 0.237 0.25074 0.2516 RANDOM 25.812
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] -0.7 -0.85 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.4 r_dihedral_angle_3_deg 11.281 r_dihedral_angle_4_deg 8.96 r_dihedral_angle_1_deg 6.816 r_long_range_B_refined 3.895 r_long_range_B_other 3.792 r_angle_refined_deg 1.536 r_angle_other_deg 0.901 r_mcangle_it 0.601 r_mcangle_other 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.4 r_dihedral_angle_3_deg 11.281 r_dihedral_angle_4_deg 8.96 r_dihedral_angle_1_deg 6.816 r_long_range_B_refined 3.895 r_long_range_B_other 3.792 r_angle_refined_deg 1.536 r_angle_other_deg 0.901 r_mcangle_it 0.601 r_mcangle_other 0.6 r_scangle_other 0.515 r_mcbond_other 0.332 r_mcbond_it 0.331 r_scbond_it 0.31 r_scbond_other 0.31 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 1812 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing