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Crystal structure of CD1a in complex with a synthetic mycobactin lipopeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ONQ PDB Entry 1ONQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 PEG 2000 MME, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.93 57.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.961 α = 90 b = 43.235 β = 91.04 c = 209.944 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD ADSC QUANTUM 210 2003-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.116 ALS 8.3.1
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 2.8 50 94.3 0.098 14.6 3 25373 23923
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 2.8 2.9 85.5 0.444 2.2 2205
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 (All) 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 PDB Entry 1ONQ 2.8 38.63 24273 22766 1157 94.29 0.21797 0.21992 0.21699 0.2263 0.27712 0.2837 RANDOM 52.263
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] 0.1 -0.04 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.574 r_dihedral_angle_3_deg 18.359 r_dihedral_angle_4_deg 12.9 r_dihedral_angle_1_deg 6.364 r_scangle_it 1.923 r_angle_refined_deg 1.478 r_scbond_it 1.108 r_angle_other_deg 0.857 r_mcangle_it 0.645 r_mcbond_it 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.574 r_dihedral_angle_3_deg 18.359 r_dihedral_angle_4_deg 12.9 r_dihedral_angle_1_deg 6.364 r_scangle_it 1.923 r_angle_refined_deg 1.478 r_scbond_it 1.108 r_angle_other_deg 0.857 r_mcangle_it 0.645 r_mcbond_it 0.3 r_nbd_refined 0.191 r_nbtor_refined 0.182 r_symmetry_vdw_other 0.18 r_nbd_other 0.178 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.148 r_symmetry_vdw_refined 0.148 r_mcbond_other 0.109 r_chiral_restr 0.084 r_nbtor_other 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6029 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 161
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing