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Crystal structure of D52N/R367Q cN-II mutant bound to dATP and free phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K7Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M MES/imidazole pH 6.5; 0.03 M of each divalent cation; 10% w/v PEG 8000, 20% v/v ethylene glycol
(Morpheus condition A2)
Crystal Properties Matthews coefficient Solvent content 3.43 64.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.579 α = 90 b = 127.104 β = 90 c = 130.317 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2015-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.736 48.99 98.8 0.093 0.101 0.998 13.6 6.5 77607 29.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.84 94.6 0.83 0.905 0.823 1.88 6.21
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 5K7Y 1.74 48.99 73724 3881 98.8 0.1797 0.1785 0.1885 0.2034 0.213 RANDOM 29.152
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.927 r_dihedral_angle_4_deg 16.702 r_dihedral_angle_3_deg 13.14 r_dihedral_angle_1_deg 6.133 r_angle_other_deg 3.598 r_angle_refined_deg 1.569 r_chiral_restr 0.096 r_gen_planes_other 0.015 r_bond_refined_d 0.013 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.927 r_dihedral_angle_4_deg 16.702 r_dihedral_angle_3_deg 13.14 r_dihedral_angle_1_deg 6.133 r_angle_other_deg 3.598 r_angle_refined_deg 1.569 r_chiral_restr 0.096 r_gen_planes_other 0.015 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3843 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing XDS data processing XSCALE data reduction Coot model building