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Crystal structure of E. coli HPPK(Y53A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G4C PDB entry 1G4C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 PEG 4000, Sodium acetate, Magnesium chloride, Glycerol, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 1.92 35.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.04 α = 90 b = 47.47 β = 108.89 c = 72.53 γ = 90
Symmetry Space Group P 1 21 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 mirrors 2000-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9B 1.0 NSLS X9B
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 1.65 34.31 98.6 0.067 13.623 2.5 32113 32113 -3 13.5
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) 1.65 1.71 99.8 0.437 2 2.4 3214
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 (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 THROUGHOUT PDB entry 1G4C 1.652 20.608 1.35 32092 32092 1000 98.31 0.162 0.162 0.16 0.1573 0.215 0.2132 Random 15.279
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] 0.898 2.572 -0.33 -0.569
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.462 f_angle_d 1.011 f_chiral_restr 0.073 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2520 Nucleic Acid Atoms Solvent Atoms 415 Heterogen Atoms 38
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing PHENIX refinement PDB_EXTRACT data extraction ADSC data collection