☰ Navigation Tabs
Crystal structure of the C-terminal domain from K. lactis Pby1, an ATP-grasp enzyme interacting with the mRNA decapping enzyme Dcp2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 295 100 mM sodium citrate tribasic pH 5.6; 0.5 M ammonium sulfate; 0.9 M lithium sulfate monohydrate
Crystal Properties Matthews coefficient Solvent content 2.13 42.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.64 α = 90 b = 95.64 β = 90 c = 75.84 γ = 120
Symmetry Space Group P 32 2 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 PIXEL DECTRIS PILATUS3 S 6M 2014-05-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97918 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.3 47.8 99.1 0.999 21.3 11.1 17920
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 0.507
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 2.3 41.41 17914 949 98.7 0.191 0.188 0.2026 0.24 0.2071 RANDOM 65.05
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] -1.1461 -1.1461 2.2923
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.74 t_omega_torsion 3.2 t_angle_deg 1.15 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.74 t_omega_torsion 3.2 t_angle_deg 1.15 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2999 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 20
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling SHARP phasing