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Structure of the Archaeal GTP:AdoCbi-P Guanylyltransferase (CobY) from Methanocaldococcus jannaschii
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 60% 2-methyl-2,4-pentanediol, 0.1M 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.94 58.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.6 α = 90 b = 63.6 β = 90 c = 222.5 γ = 120
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 SBC-3 Mirrors 2009-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9791 APS 19-BM
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 2.8 50 98.8 0.099 31.6 7.2 24528 24528
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 2.8 2.85 98.6 0.575 3.75 7.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.8 19.57 21807 21807 1098 92.7 0.25695 0.25587 0.2487 0.27873 0.2588 RANDOM 47.48
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] -0.05 -0.05 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.924 r_dihedral_angle_3_deg 7.284 r_dihedral_angle_4_deg 5.639 r_dihedral_angle_1_deg 2.377 r_angle_refined_deg 0.387 r_scangle_it 0.179 r_mcangle_it 0.162 r_scbond_it 0.108 r_mcbond_it 0.089 r_chiral_restr 0.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.924 r_dihedral_angle_3_deg 7.284 r_dihedral_angle_4_deg 5.639 r_dihedral_angle_1_deg 2.377 r_angle_refined_deg 0.387 r_scangle_it 0.179 r_mcangle_it 0.162 r_scbond_it 0.108 r_mcbond_it 0.089 r_chiral_restr 0.024 r_bond_refined_d 0.001 r_gen_planes_refined 0.001 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5634 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 128
Software Software Software Name Purpose HKL-3000 data collection SOLVE phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling