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Crystal structure of Mycoplasma pneumoniae Enolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6J36
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2M Sodium citrate tribasic dihydrate, 0.1M TRIS hydrochloride pH 8.5, 30% v/v Polyethylene glycol 400
Crystal Properties Matthews coefficient Solvent content 2.52 51.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.074 α = 90 b = 106.548 β = 103.146 c = 128.589 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 AGILENT ATLAS CCD 2018-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.8 19.84 99.6 0.997 6.4 6.4 183711 24.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 0.76
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 6J36 1.8 19.84 1.33 181623 9135 98.46 0.1909 0.1892 0.189 0.2226 0.2223 30.87
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.9665 f_angle_d 0.7871 f_chiral_restr 0.0497 f_bond_d 0.0059 f_plane_restr 0.0042
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13707 Nucleic Acid Atoms Solvent Atoms 873 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing