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Crystal structure of 2-Hydroxyisobutyryl-CoA Ligase (HCL) in the postadenylation state in complex with S3-HB-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 3.48 64.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.19 α = 90 b = 84.19 β = 90 c = 219.81 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 24.65 99.9 0.087 13.2 4.8 41011 41.66
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 99.7 0.809 2 4.8
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 24.11 40924 2056 99.7 0.209 0.208 0.2094 0.241 0.2462 RANDOM 50.17
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] -1.6149 -1.6149 3.2297
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.68 t_omega_torsion 3.33 t_angle_deg 1.02 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 18.68 t_omega_torsion 3.33 t_angle_deg 1.02 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 150 Heterogen Atoms 51
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing BUSTER refinement