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Crystal structure of dipeptide binding protein from pseudoalteromonas sp. SM9913
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DPE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 9.2 277 0.2M potassium phosphate dibasic, 20%(w/v) polyethylene glycol 3350, pH 9.2, EVAPORATION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.31 46.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.386 α = 80.03 b = 93.97 β = 84.43 c = 140.549 γ = 69.84
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 315r 2011-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9793 SSRF BL17U
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 2.288 50 95.1 185390 185390 23.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 93.6
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1dpe 2.288 42.629 0.02 185390 176680 8883 88.69 0.1946 0.1913 0.1911 0.2569 0.2534 29.32
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] 5.3673 -2.9062 -0.0214 -6.8966 -2.5764 1.5293
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.762 f_angle_d 1.183 f_chiral_restr 0.08 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32488 Nucleic Acid Atoms Solvent Atoms 1682 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MLPHARE phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling