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Crystal structure of DAPKQ23V-ADP
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 8 295 0.1 M Tris, 1.8 M Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.9 35.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.87 α = 90 b = 62.271 β = 90 c = 88.114 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 2008-08-04 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 1.49 30 99.44 11.5 7.3 42344 42344 23.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.49 1.55 94.3 3.8 6.9 2777
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 1.49 29.365 40155 2130 99.44 0.18466 0.18314 0.1835 0.21262 0.2129 RANDOM 17.893
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] -0.35 0.4 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.726 r_dihedral_angle_4_deg 20.499 r_dihedral_angle_3_deg 14.297 r_dihedral_angle_1_deg 5.443 r_scangle_it 3.446 r_scbond_it 2.124 r_mcangle_it 1.318 r_angle_refined_deg 1.305 r_mcbond_it 0.768 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.726 r_dihedral_angle_4_deg 20.499 r_dihedral_angle_3_deg 14.297 r_dihedral_angle_1_deg 5.443 r_scangle_it 3.446 r_scbond_it 2.124 r_mcangle_it 1.318 r_angle_refined_deg 1.305 r_mcbond_it 0.768 r_nbtor_refined 0.308 r_xyhbond_nbd_refined 0.223 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.192 r_symmetry_hbond_refined 0.15 r_chiral_restr 0.089 r_bond_refined_d 0.009 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_refined 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 2395 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 27
Software Software Software Name Purpose BLU-MAX data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling