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Molecular mechanism and evolution of guanylate kinase regulation by (p)ppGpp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.1 M Tris pH 8.0, 20-30% PEG3350 and 0.18-0.24 M Li2SO4 in hanging drops at 20 deg C, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.67 53.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.486 α = 90 b = 93.961 β = 111.09 c = 85.259 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 MARMOSAIC 225 mm CCD 2013-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.65 79.55 100 0.62 32.38 5 123199 123199 24.88
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 1.65 1.68 99.8 0.6 2.18 4.8 6103
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 2J41 1.65 39.26 116992 116992 6171 99.28 0.20244 0.20112 0.2122 0.22694 0.2333 RANDOM 28.528
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] 0.69 -1.34 0.66 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.142 r_dihedral_angle_4_deg 18.051 r_dihedral_angle_3_deg 14.59 r_dihedral_angle_1_deg 5.586 r_long_range_B_refined 5.224 r_long_range_B_other 5.224 r_scangle_other 2.768 r_mcangle_it 2.328 r_mcangle_other 2.328 r_scbond_it 1.643
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.142 r_dihedral_angle_4_deg 18.051 r_dihedral_angle_3_deg 14.59 r_dihedral_angle_1_deg 5.586 r_long_range_B_refined 5.224 r_long_range_B_other 5.224 r_scangle_other 2.768 r_mcangle_it 2.328 r_mcangle_other 2.328 r_scbond_it 1.643 r_scbond_other 1.643 r_mcbond_it 1.362 r_mcbond_other 1.362 r_angle_refined_deg 1.176 r_angle_other_deg 0.715 r_chiral_restr 0.069 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5999 Nucleic Acid Atoms Solvent Atoms 629 Heterogen Atoms 148
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling