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Crystal Structure of A.fulgidus Rio2 Kinase Complexed With ADP 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 3.68 293 PEG 900, SODIUM PHOSPHATE, SODIUM CITRATE , pH 3.68, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.328 α = 90 b = 44.589 β = 93.88 c = 62.63 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 2004-11-08 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 1.75 30 98.5 0.035 3.9 32601 32109 31.6
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) 1.75 1.795 87.33 0.125 3.7
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 1.75 30 30955 30487 1622 98.49 0.18491 0.1831 0.1828 0.21832 0.2177 RANDOM 25.235
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 0.64 -0.36 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.515 r_dihedral_angle_4_deg 21.216 r_dihedral_angle_3_deg 12.839 r_dihedral_angle_1_deg 5.635 r_scangle_it 4.583 r_scbond_it 2.929 r_mcangle_it 1.721 r_angle_refined_deg 1.335 r_mcbond_it 1.118 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.515 r_dihedral_angle_4_deg 21.216 r_dihedral_angle_3_deg 12.839 r_dihedral_angle_1_deg 5.635 r_scangle_it 4.583 r_scbond_it 2.929 r_mcangle_it 1.721 r_angle_refined_deg 1.335 r_mcbond_it 1.118 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.203 r_nbd_refined 0.196 r_symmetry_hbond_refined 0.183 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 2192 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling MOLREP phasing