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Crystal structure of DAPKQ23V-AMPPNP-Mg2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JKS PDB entry 1JKS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.2M CH3COOLi, 2.2 Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.91 35.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.919 α = 90 b = 62.47 β = 90 c = 88.555 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 CCD MARMOSAIC 300 mm CCD Be lenses 2008-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
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 30 99.83 13.1 7 32180 32180 27.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.65 1.71 99.83 4.7 7 3147
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 1JKS 1.65 28.62 30494 30494 1629 99.83 0.17761 0.17549 0.1744 0.21872 0.2165 RANDOM 20.918
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] -0.32 0.45 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.79 r_dihedral_angle_4_deg 19.363 r_dihedral_angle_3_deg 15.219 r_dihedral_angle_1_deg 6.002 r_scangle_it 2.339 r_mcangle_it 2.065 r_scbond_it 1.525 r_angle_refined_deg 1.486 r_mcbond_it 1.27 r_metal_ion_refined 0.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.79 r_dihedral_angle_4_deg 19.363 r_dihedral_angle_3_deg 15.219 r_dihedral_angle_1_deg 6.002 r_scangle_it 2.339 r_mcangle_it 2.065 r_scbond_it 1.525 r_angle_refined_deg 1.486 r_mcbond_it 1.27 r_metal_ion_refined 0.332 r_nbtor_refined 0.31 r_xyhbond_nbd_refined 0.237 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.204 r_symmetry_hbond_refined 0.151 r_chiral_restr 0.114 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2453 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 32
Software Software Software Name Purpose BLU-MAX data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling