☰ Navigation Tabs
1.55 Angstrom Crystal Structure of N-acetylmuramic acid 6-phosphate Etherase from Yersinia enterocolitica.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LZJ PDB entry 4LZJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 Protein: 7.6 mg/ml, 0.1 M Sodium chloride, 0.01 M Tris-HCL buffer pH(8.3), 5mM BME, Screen: JCSG+ (H7), 0.24M Ammonium sulfate, 0.1M Bis-Tris (pH 5.5), 25%(w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.34 47.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.287 α = 90 b = 81.734 β = 103.21 c = 58.848 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 MARMOSAIC 300 mm CCD Beryllium lenses 2014-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.55 30 100 0.081 0.081 15.2 4.4 125532 -3 17.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 100 0.505 0.505 2.8 4.4 6249
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4LZJ 1.55 29.95 119206 119206 6306 99.9 0.14467 0.14333 0.1557 0.17002 0.1781 RANDOM 20.071
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] -0.9 -0.37 1.5 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.302 r_dihedral_angle_4_deg 13.985 r_dihedral_angle_3_deg 10.098 r_long_range_B_refined 6.215 r_long_range_B_other 5.937 r_dihedral_angle_1_deg 3.405 r_scangle_other 2.846 r_scbond_it 1.841 r_scbond_other 1.841 r_mcangle_it 1.647
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.302 r_dihedral_angle_4_deg 13.985 r_dihedral_angle_3_deg 10.098 r_long_range_B_refined 6.215 r_long_range_B_other 5.937 r_dihedral_angle_1_deg 3.405 r_scangle_other 2.846 r_scbond_it 1.841 r_scbond_other 1.841 r_mcangle_it 1.647 r_mcangle_other 1.647 r_angle_refined_deg 1.478 r_mcbond_other 1.055 r_mcbond_it 1.054 r_angle_other_deg 0.785 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6404 Nucleic Acid Atoms Solvent Atoms 979 Heterogen Atoms 52
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling