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Crystal structure of DAPKQ23V-ADP-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 NaI, 2.2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.9 35.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.861 α = 90 b = 62.365 β = 90 c = 88.262 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 1.9 30 99.91 10.5 6.8 21031 21031 29.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.97 99.48 4.7 6.9 1469
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 PDB entry 1JKS 1.9 28.56 19907 1077 99.91 0.17289 0.17004 0.1703 0.22764 0.2303 RANDOM 22.607
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] -0.55 0.34 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.397 r_dihedral_angle_4_deg 16.012 r_dihedral_angle_3_deg 13.514 r_dihedral_angle_1_deg 4.885 r_scangle_it 2.639 r_mcangle_it 2.371 r_scbond_it 1.74 r_angle_refined_deg 1.683 r_mcbond_it 1.542 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.397 r_dihedral_angle_4_deg 16.012 r_dihedral_angle_3_deg 13.514 r_dihedral_angle_1_deg 4.885 r_scangle_it 2.639 r_mcangle_it 2.371 r_scbond_it 1.74 r_angle_refined_deg 1.683 r_mcbond_it 1.542 r_nbtor_refined 0.307 r_metal_ion_refined 0.265 r_symmetry_vdw_refined 0.264 r_symmetry_hbond_refined 0.229 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.119 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 2436 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 28
Software Software Software Name Purpose BLU-MAX data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling