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S74E dCK in complex with 5-bromodeoxycytidine and UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P5Z PDB ENTRY 1P5Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 298 12 mg/ml protein mixed with 0.9-1.5M trisodium citrate di-hydrate and 100 mM Tris, pH 7.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.18 43.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.14 α = 90 b = 69.14 β = 90 c = 118.9 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.997 69.171 99.5 0.061 37828 37632
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 1P5Z 1.997 69.171 33269 3680 97.63 0.20206 0.19707 0.1965 0.24669 0.1966 RANDOM 40.915
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] -0.8 -0.8 1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.704 r_dihedral_angle_4_deg 21.607 r_dihedral_angle_3_deg 19.198 r_dihedral_angle_1_deg 6.569 r_scangle_it 2.93 r_scbond_it 1.987 r_angle_refined_deg 1.576 r_mcangle_it 1.202 r_mcbond_it 0.696 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.704 r_dihedral_angle_4_deg 21.607 r_dihedral_angle_3_deg 19.198 r_dihedral_angle_1_deg 6.569 r_scangle_it 2.93 r_scbond_it 1.987 r_angle_refined_deg 1.576 r_mcangle_it 1.202 r_mcbond_it 0.696 r_chiral_restr 0.109 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 3901 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 84
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling