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The Structure of a Creatine_N Superfamily domain of a dipeptidase from Streptococcus thermophilus.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 297 0.1M CHES pH 9.5, 1.0M Sodium Citrate, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 3.64 66.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.503 α = 90 b = 70.503 β = 90 c = 160.388 γ = 120
Symmetry Space Group P 61 2 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 210r 2010-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97937 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 1.85 50 99.4 0.074 9.9 23.8 20449 20449 -3 29.4
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) 1.85 1.88 94.6 0.782 15.4 917
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 1.86 34.43 20287 20287 1034 98.47 0.1713 0.1713 0.1703 0.1779 0.1904 0.1977 RANDOM 35.5082
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] 1.25 0.63 1.25 -1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.19 r_dihedral_angle_3_deg 13.011 r_dihedral_angle_4_deg 12.224 r_dihedral_angle_1_deg 5.489 r_scangle_it 3.947 r_scbond_it 2.353 r_mcangle_it 1.484 r_angle_refined_deg 1.395 r_angle_other_deg 0.861 r_mcbond_it 0.809
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.19 r_dihedral_angle_3_deg 13.011 r_dihedral_angle_4_deg 12.224 r_dihedral_angle_1_deg 5.489 r_scangle_it 3.947 r_scbond_it 2.353 r_mcangle_it 1.484 r_angle_refined_deg 1.395 r_angle_other_deg 0.861 r_mcbond_it 0.809 r_mcbond_other 0.221 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1068 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 55
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building