☰ Navigation Tabs
Structure of A. thaliana 5-methylthioribose kinase in complex with ADP and MTR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OLC PDB ENTRY 2OLC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 10% PEG8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.79 55.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.46 α = 90 b = 82.24 β = 117.83 c = 91.08 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 4 mirrors 2003-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 1.0 NSLS X8C
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 1.9 80.58 98.7 0.045 16.9 3.38 83556 82470
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 1.9 1.97 90.8 0.175 4.8
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 (All) 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 2OLC 1.9 80.58 83556 78352 4105 98.66 0.16475 0.16475 0.16303 0.1632 0.19723 0.1981 RANDOM 17.312
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] -0.4 -0.27 0.72 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.042 r_dihedral_angle_4_deg 16.673 r_dihedral_angle_3_deg 11.901 r_dihedral_angle_1_deg 5.907 r_scangle_it 3.199 r_scbond_it 2.098 r_angle_refined_deg 1.38 r_mcangle_it 1.196 r_mcbond_it 0.819 r_symmetry_hbond_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.042 r_dihedral_angle_4_deg 16.673 r_dihedral_angle_3_deg 11.901 r_dihedral_angle_1_deg 5.907 r_scangle_it 3.199 r_scbond_it 2.098 r_angle_refined_deg 1.38 r_mcangle_it 1.196 r_mcbond_it 0.819 r_symmetry_hbond_refined 0.317 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.214 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.095 r_metal_ion_refined 0.068 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6650 Nucleic Acid Atoms Solvent Atoms 778 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing