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Crystal Structure of A.fulgidus Rio1 serine protein kinase bound to ADP and Manganese ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZTF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 PEG 4000, MES, Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 46.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.414 α = 90 b = 80.084 β = 90.17 c = 121.056 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 100 CCD 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 1.89 30 0.147 81701 78499
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) 1.89 1.939 79.58 0.35 6.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1ZTF 1.89 30 81701 74564 3935 96.07 0.19224 0.18862 0.26215 0.2013 RANDOM 30.063
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] -1.7 -0.48 3.45 -1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.316 r_dihedral_angle_4_deg 17.738 r_dihedral_angle_3_deg 16.455 r_scangle_it 7.173 r_dihedral_angle_1_deg 5.808 r_scbond_it 5.14 r_mcangle_it 3.051 r_mcbond_it 2.323 r_angle_refined_deg 1.602 r_nbtor_refined 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.316 r_dihedral_angle_4_deg 17.738 r_dihedral_angle_3_deg 16.455 r_scangle_it 7.173 r_dihedral_angle_1_deg 5.808 r_scbond_it 5.14 r_mcangle_it 3.051 r_mcbond_it 2.323 r_angle_refined_deg 1.602 r_nbtor_refined 0.33 r_symmetry_vdw_refined 0.293 r_nbd_refined 0.263 r_symmetry_hbond_refined 0.234 r_xyhbond_nbd_refined 0.226 r_chiral_restr 0.126 r_bond_refined_d 0.016 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 7830 Nucleic Acid Atoms Solvent Atoms 822 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data scaling MOLREP phasing