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X-ray structural studies of the entire extra-cellular region of the Ser/Thr kinase PrkC from Staphylococcus aureus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 5 mg/mL protein solution, 21% (w/v) MPEG2000, 3% w/v D-(+)-galactose, 160 mM ammonium sulfate and 60 mM sodium acetate trihydrate buffer, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.62 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.681 α = 90 b = 69.103 β = 90 c = 88.43 γ = 90
Symmetry Space Group P 21 21 2
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 RIGAKU SATURN 92 2010-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.2 30 99.9 0.08 18064 18045
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.28 99.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.2 9.97 17925 15327 829 91.29 0.24674 0.24426 0.29346 0.2795 RANDOM 42.559
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] -0.04 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.673 r_dihedral_angle_3_deg 17.809 r_dihedral_angle_4_deg 15.275 r_dihedral_angle_1_deg 6.427 r_scangle_it 2.771 r_scbond_it 1.702 r_mcangle_it 1.327 r_angle_refined_deg 1.286 r_mcbond_it 0.762 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.673 r_dihedral_angle_3_deg 17.809 r_dihedral_angle_4_deg 15.275 r_dihedral_angle_1_deg 6.427 r_scangle_it 2.771 r_scbond_it 1.702 r_mcangle_it 1.327 r_angle_refined_deg 1.286 r_mcbond_it 0.762 r_nbtor_refined 0.3 r_nbd_refined 0.235 r_symmetry_vdw_refined 0.234 r_xyhbond_nbd_refined 0.2 r_symmetry_hbond_refined 0.175 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 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 2180 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 4
Software Software Software Name Purpose HKL-2000 data collection Auto-Rickshaw phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling