☰ Navigation Tabs
Crystal Structure of the peptide binding protein DppE from Bacillus subtilis in complex with murein tripeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FAJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 Crystals of DppE suitable for X-ray analysis were obtained from hanging drops formed by mixing 1 mircol of reservoir solution containing 0.1 M Bis-Tris-Propane pH 8.5, 0.4 M MgCl2, 22.5 % PEG 3350 and 2.5 % DMSO with 1 microl of protein at 13 mg.ml-1 .
Crystal Properties Matthews coefficient Solvent content 2.23 44.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.855 α = 78.088 b = 61.31 β = 82.672 c = 124.073 γ = 61.597
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 PILATUS 6M 2015-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.51 60.74 96.3 0.053 0.075 0.053 0.998 8.4 2.2 233391
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.54 0.759 1.073 0.759 0.572 2.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4FAJ 1.51 60.739 233390 11490 96.293 0.186 0.1845 0.1864 0.2213 0.2233 24.662
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] -0.88 -0.029 1.355 0.324 -2.004 -0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.169 r_dihedral_angle_3_deg 14.104 r_dihedral_angle_1_deg 6.697 r_dihedral_angle_2_deg 5.743 r_lrange_it 5.686 r_lrange_other 5.685 r_scangle_it 4.24 r_scangle_other 4.24 r_scbond_it 2.86 r_scbond_other 2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.169 r_dihedral_angle_3_deg 14.104 r_dihedral_angle_1_deg 6.697 r_dihedral_angle_2_deg 5.743 r_lrange_it 5.686 r_lrange_other 5.685 r_scangle_it 4.24 r_scangle_other 4.24 r_scbond_it 2.86 r_scbond_other 2.86 r_mcangle_it 2.835 r_mcangle_other 2.835 r_mcbond_it 2.073 r_mcbond_other 2.072 r_angle_refined_deg 1.502 r_angle_other_deg 0.522 r_symmetry_xyhbond_nbd_refined 0.278 r_nbd_refined 0.223 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.181 r_nbd_other 0.179 r_symmetry_nbd_refined 0.168 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.079 r_symmetry_xyhbond_nbd_other 0.044 r_metal_ion_refined 0.024 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_xyhbond_nbd_other 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11876 Nucleic Acid Atoms Solvent Atoms 1206 Heterogen Atoms 177
Software Software Software Name Purpose REFMAC refinement REFMAC refinement autoPROC data processing XDS data reduction Aimless data scaling MOLREP phasing