☰ Navigation Tabs
Crystal structure of thymidylate kinase from Ehrlichia chaffeensis at 2.15A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PBR PDB ENTRY 2PBR MODIFIED WITH CCP4 PROGRAM CHAINSAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 MD PACT SCREEN G8: 100MM BIS-TRIS-PROPANE PH 7.5, 200MM NA-SULPHATE, 20% PEG 3350; EHCHA.01616.A AT 25.5MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 2.04 39.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.17 α = 90 b = 144.82 β = 90 c = 146.84 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 ADSC QUANTUM 315r Single crystal, cylindrically bent, Si(220) 2009-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9744 ALS 5.0.1
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 2.15 50 100 0.079 16.84 5.9 46727 46708 -3
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 2.15 2.21 99.9 0.481 3.7 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2PBR MODIFIED WITH CCP4 PROGRAM CHAINSAW 2.15 46.37 46727 44279 2354 99.97 0.18883 0.18656 0.1981 0.2322 0.2488 RANDOM 31.523
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] 0.47 -2.03 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.035 r_dihedral_angle_4_deg 22.633 r_dihedral_angle_3_deg 13.267 r_dihedral_angle_1_deg 5.192 r_scangle_it 3.36 r_scbond_it 2.112 r_angle_refined_deg 1.345 r_mcangle_it 1.295 r_angle_other_deg 0.906 r_mcbond_it 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.035 r_dihedral_angle_4_deg 22.633 r_dihedral_angle_3_deg 13.267 r_dihedral_angle_1_deg 5.192 r_scangle_it 3.36 r_scbond_it 2.112 r_angle_refined_deg 1.345 r_mcangle_it 1.295 r_angle_other_deg 0.906 r_mcbond_it 0.71 r_mcbond_other 0.208 r_chiral_restr 0.076 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5700 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 28
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling