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Crystal Structure of the C-terminal domain of AcKRS-1 bound with N-acetyl-lysine and ADPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q7G PDB ENTRY 2Q7G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 50 mM Tris, pH 8.0, 23% PEG2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.66 66.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.031 α = 90 b = 105.031 β = 90 c = 70.731 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 ADSC QUANTUM 315r 2008-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0809 NSLS X29A
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 2.248 90.909 98.7 0.048 41.2 7.5 21278 21010 2.6 2.6
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 2.248 2.33 90.6 0.538 2.6 5.3
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 PDB ENTRY 2Q7G 2.25 90.909 21010 19912 1079 98.66 0.18737 0.18593 0.21443 0.2175 RANDOM 60.752
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] -1.14 -0.57 -1.14 3.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.496 r_dihedral_angle_4_deg 12.981 r_dihedral_angle_3_deg 12.261 r_dihedral_angle_1_deg 5.818 r_mcangle_it 4.81 r_mcbond_it 2.784 r_mcbond_other 2.778 r_scbond_it 2.658 r_angle_refined_deg 1.092 r_angle_other_deg 0.684
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.496 r_dihedral_angle_4_deg 12.981 r_dihedral_angle_3_deg 12.261 r_dihedral_angle_1_deg 5.818 r_mcangle_it 4.81 r_mcbond_it 2.784 r_mcbond_other 2.778 r_scbond_it 2.658 r_angle_refined_deg 1.092 r_angle_other_deg 0.684 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.003 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2167 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 68
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling