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Crystal Structure of N-acetylneuraminate lyase from Mycoplasma synoviae, crystal form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N4P PDB entry 4N4P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 50 mM MES, pH 6.0, 50 % MPD, vapor diffusion, sitting drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.44 49.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.225 α = 90 b = 142.441 β = 108.27 c = 80.792 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 PIXEL DECTRIS PILATUS 6M 2013-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.89997 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 76.718 99 0.113 6.7 3.5 85882 85882 -3 -3 27.878
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 2 2.11 97.6 0.499 0.499 1.5 3.3 12324
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 4N4P 2 30 85788 81494 4294 98.86 0.2413 0.2392 0.2401 0.283 0.2829 RANDOM 27.5753
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] 1.52 -0.93 -1.8 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.164 r_dihedral_angle_3_deg 15.838 r_dihedral_angle_4_deg 14.017 r_dihedral_angle_1_deg 6.151 r_scangle_it 2.828 r_scbond_it 1.861 r_angle_refined_deg 1.315 r_mcangle_it 1.179 r_mcbond_it 0.659 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.164 r_dihedral_angle_3_deg 15.838 r_dihedral_angle_4_deg 14.017 r_dihedral_angle_1_deg 6.151 r_scangle_it 2.828 r_scbond_it 1.861 r_angle_refined_deg 1.315 r_mcangle_it 1.179 r_mcbond_it 0.659 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9342 Nucleic Acid Atoms Solvent Atoms 482 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction