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Crystal Structure of Weissella viridescens FemX:UDP-MurNAc-pentapeptide complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NE9 PDB ENTRY 1NE9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 PEG 2K, NaCl, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.23 44.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.201 α = 90 b = 100.61 β = 115.64 c = 46.538 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 MARRESEARCH two crystals monochromator between two cylindrical parabolic mirrors 2002-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979711 ESRF BM30A
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 1.9 15.57 98.6 0.073 7.5 3.6 27221 12.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 98 0.19 3.7 3.8 3947
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 difference fourier synthesis THROUGHOUT PDB ENTRY 1NE9 1.9 15.57 27014 1351 97.9 0.185 0.172 0.172 0.1726 0.207 0.2063 RANDOM 16.3
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] -2.08 3.16 -0.35 2.43
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.8 c_scangle_it 2.6 c_mcangle_it 2.48 c_mcbond_it 1.9 c_scbond_it 1.8 c_angle_deg 1.3 c_improper_angle_d 0.82 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2763 Nucleic Acid Atoms Solvent Atoms 466 Heterogen Atoms 15
Software Software Software Name Purpose CNS refinement MOSFLM data reduction CCP4 data scaling CNS phasing