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Crystal structure of 2-Hydroxyisobutyryl-CoA Ligase (HCL) in the postadenylation state in complex with R3-HIB-AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y4N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.05 M MES PH 6.0, 2.1 M LITHIUM
SULFATE, 0.01 M MAGNESIUM CHLORIDE, VAPOR DIFFUSION, HANGING
DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 3.45 64.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.86 α = 90 b = 83.86 β = 90 c = 219.7 γ = 90
Symmetry Space Group P 41 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 PIXEL DECTRIS PILATUS3 6M 2013-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918 BESSY 14.1
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 24.58 99.8 0.107 11.9 5.7 40737 40.78
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 2.2 2.32 99.4 0.897 2 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 2Y4N 2.2 22.18 40637 2062 99.8 0.207 0.206 0.2021 0.238 0.24 RANDOM 47.17
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] -1.4765 -1.4765 2.9529
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.45 t_omega_torsion 3.43 t_angle_deg 1.03 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.45 t_omega_torsion 3.43 t_angle_deg 1.03 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 3737 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 36
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing BUSTER refinement