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Crystal Structure of the peptide binding protein DppE from Bacillus subtilis in the unliganded state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AY0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 Ligand free DppE was crystallised in a sitting drop formed by mixing 150 nl of the unliganded protein at 9 mg.ml-1 with 150 nl of 0.1 M MIB buffer pH 4.0, 25 % (w/v) PEG 1500.
Crystal Properties Matthews coefficient Solvent content 2.23 44.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.53 α = 90 b = 91.08 β = 90 c = 106.74 γ = 90
Symmetry Space Group P 21 21 21
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 2016-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 1.4 46.09 99.6 0.046 0.053 0.026 0.999 20.9 7.4 104801
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 1.4 1.42 0.344 0.436 0.262 0.886 4.4
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 8AY0 1.4 46.089 104711 5232 99.491 0.182 0.1806 0.1763 0.2084 0.2037 16.093
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] -0.239 -0.319 0.558
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.407 r_dihedral_angle_3_deg 13.087 r_dihedral_angle_1_deg 6.4 r_dihedral_angle_2_deg 5.791 r_lrange_it 5.46 r_lrange_other 5.279 r_scangle_it 4.219 r_scangle_other 4.218 r_scbond_it 2.888 r_scbond_other 2.883
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.407 r_dihedral_angle_3_deg 13.087 r_dihedral_angle_1_deg 6.4 r_dihedral_angle_2_deg 5.791 r_lrange_it 5.46 r_lrange_other 5.279 r_scangle_it 4.219 r_scangle_other 4.218 r_scbond_it 2.888 r_scbond_other 2.883 r_mcangle_other 2.425 r_mcangle_it 2.423 r_angle_refined_deg 1.81 r_mcbond_it 1.657 r_mcbond_other 1.655 r_angle_other_deg 0.593 r_symmetry_xyhbond_nbd_refined 0.34 r_symmetry_nbd_refined 0.243 r_nbd_refined 0.231 r_symmetry_nbd_other 0.189 r_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.183 r_nbd_other 0.168 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4029 Nucleic Acid Atoms Solvent Atoms 513 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement REFMAC refinement autoPROC data processing XDS data reduction Aimless data scaling MOLREP phasing