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Crystal structure of DAPKL93G with N6-cyclopentyladenosine
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, HANGING DROP 7.5 295 100 mM Tris, 1.1 ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.94 36.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.109 α = 90 b = 62.745 β = 90 c = 88.785 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 225 mm CCD 2006-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM APS 22-BM
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 1.6 50 99.24 22.5 5.1 35255 35255 26.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.66 92.89 3.59 2.9 3329
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 1.6 26.76 33436 1763 99.24 0.20329 0.20141 0.201 0.2389 0.2398 RANDOM 20.906
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] 0.36 0.31 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.582 r_dihedral_angle_4_deg 17.779 r_dihedral_angle_3_deg 15.426 r_dihedral_angle_1_deg 7.595 r_scangle_it 3.579 r_scbond_it 2.271 r_mcangle_it 1.59 r_angle_refined_deg 1.576 r_mcbond_it 0.928 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.582 r_dihedral_angle_4_deg 17.779 r_dihedral_angle_3_deg 15.426 r_dihedral_angle_1_deg 7.595 r_scangle_it 3.579 r_scbond_it 2.271 r_mcangle_it 1.59 r_angle_refined_deg 1.576 r_mcbond_it 0.928 r_nbtor_refined 0.31 r_nbd_refined 0.223 r_symmetry_vdw_refined 0.183 r_chiral_restr 0.145 r_symmetry_hbond_refined 0.144 r_xyhbond_nbd_refined 0.122 r_bond_refined_d 0.011 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_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 2372 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 24
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling