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Crystal structure of DAPKL93G complexed with N6-(2-Phenylethyl)adenosine
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 100mM Tris, 1.1 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.92 36.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.839 α = 90 b = 62.881 β = 90 c = 88.467 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 100 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 1.71 50 98.86 12.5 5.1 28631 29.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.71 1.77 92.71 2.42 4.7 5008
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 1.71 44.237 27172 1460 98.86 0.19686 0.19456 0.1943 0.23889 0.2386 RANDOM 22.039
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] 0.5 -0.08 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.223 r_dihedral_angle_4_deg 18.662 r_dihedral_angle_3_deg 14.76 r_dihedral_angle_1_deg 9.232 r_scangle_it 3.736 r_scbond_it 2.386 r_mcangle_it 1.611 r_angle_refined_deg 1.561 r_mcbond_it 0.927 r_xyhbond_nbd_refined 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.223 r_dihedral_angle_4_deg 18.662 r_dihedral_angle_3_deg 14.76 r_dihedral_angle_1_deg 9.232 r_scangle_it 3.736 r_scbond_it 2.386 r_mcangle_it 1.611 r_angle_refined_deg 1.561 r_mcbond_it 0.927 r_xyhbond_nbd_refined 0.52 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.246 r_nbd_refined 0.229 r_symmetry_hbond_refined 0.166 r_chiral_restr 0.143 r_bond_refined_d 0.013 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 2324 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 32
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling