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C4S dCK variant of dCK in complex with D-dG+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, HANGING DROP 7.5 285 1.0M Sodium Citrate, 100mM Hepes, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 1.99 38.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.8 α = 90 b = 107.5 β = 90 c = 110.4 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 2006-02-23 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 Merge 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 1.97 30 96 0.091 10.1 7 36226 36226
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.97 2 79.4 0.458 3.1 3.3 1316
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 1.97 30 32619 3607 96.04 0.21127 0.20606 0.2069 0.25877 0.2569 RANDOM 28.641
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] -0.93 1.99 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.649 r_dihedral_angle_4_deg 22.009 r_dihedral_angle_3_deg 18.126 r_dihedral_angle_1_deg 6.031 r_scangle_it 3.739 r_scbond_it 2.559 r_mcangle_it 1.762 r_angle_refined_deg 1.635 r_mcbond_it 1.055 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.649 r_dihedral_angle_4_deg 22.009 r_dihedral_angle_3_deg 18.126 r_dihedral_angle_1_deg 6.031 r_scangle_it 3.739 r_scbond_it 2.559 r_mcangle_it 1.762 r_angle_refined_deg 1.635 r_mcbond_it 1.055 r_nbtor_refined 0.318 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.186 r_xyhbond_nbd_refined 0.179 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.116 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3525 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement SERGUI data collection XDS data reduction XDS data scaling MOLREP phasing