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C4S dCK variant of dCK in complex with cladribine+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 2.16 43.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.76 α = 90 b = 44.09 β = 95.71 c = 94.64 γ = 90
Symmetry Space Group P 1 21 1
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 2005-12-11 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 1.79 30 99.4 0.114 11.7 6.1 52169 52169
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) 1.79 1.9 96.9 0.627 3.3 5.6 8138
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 1.8 30 46591 5225 99.17 0.20695 0.20218 0.2008 0.24991 0.2489 RANDOM 23.586
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] 1.19 -0.21 -0.93 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.524 r_dihedral_angle_4_deg 18.699 r_dihedral_angle_3_deg 16.028 r_dihedral_angle_1_deg 5.726 r_scangle_it 3.614 r_scbond_it 2.704 r_mcangle_it 1.71 r_angle_refined_deg 1.552 r_mcbond_it 1.048 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.524 r_dihedral_angle_4_deg 18.699 r_dihedral_angle_3_deg 16.028 r_dihedral_angle_1_deg 5.726 r_scangle_it 3.614 r_scbond_it 2.704 r_mcangle_it 1.71 r_angle_refined_deg 1.552 r_mcbond_it 1.048 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.117 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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 3644 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement SERGUI data collection XDS data reduction XDS data scaling MOLREP phasing