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Crystal structure of Bacillus anthracis transpeptidase enzyme CapD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GA9 PDB entry 3GA9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 15% PEG 3350, 8% PEG 400, 0.05M LiSO4, 0.1M Na-Hepes pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.2 44.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.668 α = 90 b = 120.621 β = 90.87 c = 77.375 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 ADSC QUANTUM 315 mirrors 2006-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
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 1.79 50 98 0.117 16.1 4.7 88013 83551
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 1.79 1.83 82.9 0.555 1.73 4
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 (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 3GA9 1.79 40.69 83551 83551 4413 97.58 0.19875 0.19653 0.2018 0.24166 0.2477 RANDOM 22.615
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] -1.4 0.25 3.42 -2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.55 r_dihedral_angle_3_deg 15.673 r_dihedral_angle_4_deg 14.886 r_dihedral_angle_1_deg 8.15 r_scangle_it 3.189 r_scbond_it 2.367 r_angle_refined_deg 1.587 r_mcangle_it 1.549 r_mcbond_it 1.222 r_angle_other_deg 0.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.55 r_dihedral_angle_3_deg 15.673 r_dihedral_angle_4_deg 14.886 r_dihedral_angle_1_deg 8.15 r_scangle_it 3.189 r_scbond_it 2.367 r_angle_refined_deg 1.587 r_mcangle_it 1.549 r_mcbond_it 1.222 r_angle_other_deg 0.968 r_mcbond_other 0.237 r_nbd_refined 0.222 r_symmetry_vdw_other 0.211 r_symmetry_hbond_refined 0.198 r_nbd_other 0.194 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.177 r_symmetry_vdw_refined 0.126 r_chiral_restr 0.101 r_nbtor_other 0.088 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6904 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 19
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling