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Crystal Structure of full-legnth A.fulgidus Rio1 Serine Kinase bound to ATP and Mn2+ ions.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZTF PDB entry 1ZTF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.3 293 PEG 4000, Ammonium Sulfate, MES, pH 6.3, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.306 α = 90 b = 80.373 β = 90.02 c = 121.32 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 IMAGE PLATE MARRESEARCH 2004-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.96860 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 2 30 0.106 11.2 3.8 69295 63199
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 1ZTF 2 30 62837 60003 3196 91.19 0.18067 0.17702 0.1787 0.2488 0.2492 RANDOM 23.419
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] -1.54 -0.07 2.95 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.617 r_dihedral_angle_4_deg 19.821 r_dihedral_angle_3_deg 17.077 r_dihedral_angle_1_deg 6.189 r_scangle_it 4.501 r_scbond_it 3.04 r_angle_refined_deg 1.679 r_mcangle_it 1.66 r_mcbond_it 1.205 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.617 r_dihedral_angle_4_deg 19.821 r_dihedral_angle_3_deg 17.077 r_dihedral_angle_1_deg 6.189 r_scangle_it 4.501 r_scbond_it 3.04 r_angle_refined_deg 1.679 r_mcangle_it 1.66 r_mcbond_it 1.205 r_nbtor_refined 0.313 r_nbd_refined 0.234 r_symmetry_hbond_refined 0.234 r_symmetry_vdw_refined 0.211 r_xyhbond_nbd_refined 0.209 r_chiral_restr 0.112 r_bond_refined_d 0.018 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 7835 Nucleic Acid Atoms Solvent Atoms 916 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data scaling MOLREP phasing