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4-Chlorobenzoyl-CoA Ligase/Synthetase, Mutant D402P, bound to 4CB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T5D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 277 16-24% pentaerythritol propoxylate 426
0.1 M HEPES
1mM ATP
1mM 4CB, pH 6.5, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.09 60.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.922 α = 90 b = 127.922 β = 90 c = 71.23 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 113 CCD ADSC QUANTUM 210 2005-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F2 .97934 CHESS F2
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 2.6 30 94.8 0.072 22.4 8.8 19751
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) 2.6 2.667 96.1 0.479 2.6
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 IT5D 2.6 30 18725 992 94.12 0.20837 0.20611 0.2825 0.25216 0.3177 RANDOM 51.908
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] -0.14 -0.07 -0.14 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.898 r_dihedral_angle_3_deg 15.108 r_dihedral_angle_4_deg 11.676 r_dihedral_angle_1_deg 5.178 r_mcangle_it 1.825 r_scangle_it 1.784 r_scbond_it 1.15 r_mcbond_it 1.136 r_angle_refined_deg 1.015 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.898 r_dihedral_angle_3_deg 15.108 r_dihedral_angle_4_deg 11.676 r_dihedral_angle_1_deg 5.178 r_mcangle_it 1.825 r_scangle_it 1.784 r_scbond_it 1.15 r_mcbond_it 1.136 r_angle_refined_deg 1.015 r_nbtor_refined 0.298 r_nbd_refined 0.185 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.116 r_symmetry_hbond_refined 0.113 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 3735 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement CHESS data collection MOSFLM data reduction SCALA data scaling MOLREP phasing