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Crystal structure of the peptide binding protein, OppA, from Bacillus subtilis in complex with an endogenous tetrapeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RKM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 Crystals of OppA were obtained from hanging drops composed of 2 microlitres of reservoir solution consisting of 0.1 M MMT, 22.5% PEG 1500 and 2.5% DMSO pH 8.0 and 2 microlitres protein at 18 mg.ml-1 with crystal optimisation following a seeding protocol.
Crystal Properties Matthews coefficient Solvent content 2.11 41.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.52 α = 90 b = 65.89 β = 100.97 c = 153.29 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 6M 2015-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.82 Diamond I03
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 1.5 55.025 99.9 0.045 0.059 0.038 0.998 12.6 4.2 158694
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 1.5 1.53 0.723 0.955 0.617 0.609 4.2
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 1RKM 1.5 55.025 158693 7849 99.861 0.179 0.1772 0.1768 0.2066 0.2053 22.694
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] -0.661 -0.283 1.266 -0.461
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.093 r_dihedral_angle_6_deg 16.002 r_lrange_other 15.461 r_dihedral_angle_3_deg 13.791 r_dihedral_angle_2_deg 7.4 r_dihedral_angle_1_deg 6.494 r_scangle_it 4.666 r_scangle_other 4.666 r_scbond_it 3.151 r_scbond_other 3.151
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.093 r_dihedral_angle_6_deg 16.002 r_lrange_other 15.461 r_dihedral_angle_3_deg 13.791 r_dihedral_angle_2_deg 7.4 r_dihedral_angle_1_deg 6.494 r_scangle_it 4.666 r_scangle_other 4.666 r_scbond_it 3.151 r_scbond_other 3.151 r_mcangle_it 2.561 r_mcangle_other 2.561 r_mcbond_it 1.975 r_mcbond_other 1.974 r_angle_refined_deg 1.614 r_angle_other_deg 0.557 r_symmetry_nbd_refined 0.234 r_nbd_refined 0.221 r_symmetry_nbd_other 0.193 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.182 r_nbd_other 0.178 r_symmetry_xyhbond_nbd_refined 0.177 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_xyhbond_nbd_other 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8171 Nucleic Acid Atoms Solvent Atoms 884 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data reduction DIALS data reduction Aimless data scaling PHASER phasing