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The structure of the oligopeptide-binding protein, AppA, from Bacillus subtilis in complex with a nonapeptide.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DPE pdb entry 1DPE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 PEG8000, zinc acetate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.6 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.955 α = 90 b = 90.779 β = 90 c = 54.719 γ = 90
Symmetry Space Group P 21 21 2
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 4 mirrors 2002-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 0.97920 SRS PX14.2
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 1.55 50 97.3 0.081 18.5 88121 88121
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 1.55 1.61 72.6 0.788 1.6 6467
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 (All) 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 + MIR THROUGHOUT pdb entry 1DPE 1.55 30.57 83608 83608 4411 100 0.17703 0.17703 0.17552 0.235 0.20593 0.2561 RANDOM 27.752
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] -0.02 -0.31 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.508 r_dihedral_angle_3_deg 13.875 r_dihedral_angle_4_deg 12.466 r_dihedral_angle_1_deg 6.008 r_scangle_it 3.462 r_scbond_it 2.452 r_angle_refined_deg 1.469 r_mcangle_it 1.26 r_angle_other_deg 1.12 r_mcbond_it 1.048
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.508 r_dihedral_angle_3_deg 13.875 r_dihedral_angle_4_deg 12.466 r_dihedral_angle_1_deg 6.008 r_scangle_it 3.462 r_scbond_it 2.452 r_angle_refined_deg 1.469 r_mcangle_it 1.26 r_angle_other_deg 1.12 r_mcbond_it 1.048 r_symmetry_vdw_refined 0.302 r_symmetry_hbond_refined 0.265 r_mcbond_other 0.218 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.214 r_nbtor_refined 0.184 r_nbd_other 0.177 r_symmetry_vdw_other 0.149 r_chiral_restr 0.124 r_metal_ion_refined 0.095 r_nbtor_other 0.086 r_bond_refined_d 0.013 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_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4164 Nucleic Acid Atoms Solvent Atoms 441 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing MLPHARE phasing