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Crystal Structure of A.fulgidus Rio2 Kinase Complexed With ATP and Manganese Ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TQI PDB entry 1TQI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.78 293 PEG 900, SODIUM PHOSPHATE, SODIUM CITRATE , pH 3.78, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 51.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.862 α = 90 b = 44.365 β = 94.01 c = 62.793 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 MARRESEARCH 2004-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.99997 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.84 63.25 0.035 3.9 28175 27131
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.84 1.887 68.2 0.114 3.8
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 1TQI 1.84 63.25 26765 27131 1361 96.25 0.1835 0.1835 0.183 0.2124 0.1995 RANDOM 25.191
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] -0.48 0.84 -0.47 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.587 r_dihedral_angle_4_deg 18.955 r_dihedral_angle_3_deg 14.071 r_dihedral_angle_1_deg 5.713 r_scangle_it 4.53 r_scbond_it 2.892 r_mcangle_it 1.753 r_angle_refined_deg 1.414 r_mcbond_it 1.159 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.587 r_dihedral_angle_4_deg 18.955 r_dihedral_angle_3_deg 14.071 r_dihedral_angle_1_deg 5.713 r_scangle_it 4.53 r_scbond_it 2.892 r_mcangle_it 1.753 r_angle_refined_deg 1.414 r_mcbond_it 1.159 r_nbtor_refined 0.307 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.199 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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 2204 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling MOLREP phasing