☰ Navigation Tabs
Crystal structure of dipeptidase from Streptomyces coelicolor complexed with phosphinate pseudodipeptide L-Leu-D-Ala
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K5X PDB ENTRY 3K5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 22% Polyacrylic Acid, 0.1M Hepes, 0.2M magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 3.29 62.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.043 α = 90 b = 97.043 β = 90 c = 104.962 γ = 120
Symmetry Space Group P 31 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 4 2009-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97915 NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.297 27.175 92.52 130593 130593
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 3K5X 1.297 27.175 130593 130593 6571 92.52 0.1711 0.1711 0.1707 0.1649 0.1772 0.1718 RANDOM
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] -1.5578 -1.5578 3.1156
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.411 f_angle_d 1.075 f_chiral_restr 0.072 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2990 Nucleic Acid Atoms Solvent Atoms 543 Heterogen Atoms 41
Software Software Software Name Purpose ADSC data collection BALBES phasing PHENIX refinement DENZO data reduction SCALEPACK data scaling