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N-terminal domain of Xaa-Pro dipeptidase from Lactobacillus brevis.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.1 M Tris buffer, 0.2 M ammonium sulfate, 25% PEG-3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.03 39.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.867 α = 90 b = 50.962 β = 104.33 c = 49.289 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 CCD ADSC QUANTUM 210r 2009-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9792 APS 19-BM
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 1.46 36.5 99.9 0.053 14.6 9.1 22642 22642 27
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 1.46 1.49 98.8 0.55 2.05 3.2 1115
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.46 36.5 22596 22596 1149 99.43 0.164 0.164 0.163 0.1771 0.198 0.203 RANDOM 16.355
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] 0.37 0.38 -0.33 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.96 r_dihedral_angle_4_deg 26.763 r_dihedral_angle_3_deg 13.664 r_dihedral_angle_1_deg 6.072 r_scangle_it 4.123 r_scbond_it 2.71 r_mcangle_it 1.803 r_angle_refined_deg 1.791 r_mcbond_it 1.107 r_angle_other_deg 0.998
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.96 r_dihedral_angle_4_deg 26.763 r_dihedral_angle_3_deg 13.664 r_dihedral_angle_1_deg 6.072 r_scangle_it 4.123 r_scbond_it 2.71 r_mcangle_it 1.803 r_angle_refined_deg 1.791 r_mcbond_it 1.107 r_angle_other_deg 0.998 r_mcbond_other 0.364 r_chiral_restr 0.109 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1077 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling SHELXD phasing MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing HKL-3000 phasing