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Crystal structure of biotin protein ligase (RV3279C) of Mycobacterium tuberculosis, complexed with biotinyl-5'-AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CGH PDB ENTRY 2CGH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293 0.1 M Tris-HCl, pH 7.8, 0.2 M lithium sulfate, 25% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.14 42.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.737 α = 90 b = 75.406 β = 97.92 c = 77.599 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 100 CCD MAR CCD 165 mm mirrors: 1: Rh-coated, zerodur, vertical focusing possible, 2: Rh-coated, zerodur, vertically focusing 2006-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.9762 EMBL/DESY, HAMBURG BW7A
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 1.7 31.36 97.4 0.098 15.6 12 51119 2 2 24.2
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 1.7 1.8 95.9 0.526 3.25 7.1 7904
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 PDB ENTRY 2CGH 1.7 31.36 48546 2550 100 0.194 0.192 0.2 0.242 0.2499 RANDOM 28.938
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] -0.39 -0.58 1.37 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.506 r_dihedral_angle_4_deg 18.981 r_dihedral_angle_3_deg 13.586 r_dihedral_angle_1_deg 6.753 r_scangle_it 3.199 r_scbond_it 2.227 r_angle_refined_deg 1.749 r_mcangle_it 1.401 r_angle_other_deg 1.001 r_mcbond_it 0.916
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.506 r_dihedral_angle_4_deg 18.981 r_dihedral_angle_3_deg 13.586 r_dihedral_angle_1_deg 6.753 r_scangle_it 3.199 r_scbond_it 2.227 r_angle_refined_deg 1.749 r_mcangle_it 1.401 r_angle_other_deg 1.001 r_mcbond_it 0.916 r_symmetry_vdw_refined 0.324 r_mcbond_other 0.287 r_symmetry_vdw_other 0.261 r_symmetry_hbond_refined 0.248 r_nbd_refined 0.221 r_nbd_other 0.217 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.171 r_chiral_restr 0.111 r_nbtor_other 0.09 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3776 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 81
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling