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Crystal structure of ethanolamine ammonia-lyase heavy chain (YP_013784.1) from Listeria monocytogenes 4b F2365 at 2.15 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 NANODROP, 30.0% 2-methyl-2,4-pentanediol, 0.2M Magnesium acetate, 0.1M Sodium pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.28 46.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.33 α = 90 b = 223.7 β = 90 c = 65.93 γ = 90
Symmetry Space Group P 21 21 2
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 325 mm CCD Flat mirror (vertical focusing) 2007-02-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91162, 0.97925, 0.97895 SSRL BL11-1
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 2.15 29.21 98.9 0.054 9.26 162506 -3 44.807
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 2.15 2.17 94.6 0.487 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 2.15 29.21 161942 8067 99.27 0.23 0.228 0.238 0.279 0.2878 RANDOM 48.229
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] -2.31 -1.03 3.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.243 r_dihedral_angle_4_deg 15.271 r_dihedral_angle_3_deg 11.528 r_scangle_it 6.576 r_scbond_it 4.918 r_dihedral_angle_1_deg 3.402 r_mcangle_it 2.663 r_mcbond_it 1.662 r_angle_refined_deg 1.594 r_angle_other_deg 1.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.243 r_dihedral_angle_4_deg 15.271 r_dihedral_angle_3_deg 11.528 r_scangle_it 6.576 r_scbond_it 4.918 r_dihedral_angle_1_deg 3.402 r_mcangle_it 2.663 r_mcbond_it 1.662 r_angle_refined_deg 1.594 r_angle_other_deg 1.085 r_mcbond_other 0.685 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.197 r_symmetry_vdw_other 0.189 r_nbtor_refined 0.178 r_symmetry_hbond_refined 0.169 r_nbd_other 0.161 r_symmetry_vdw_refined 0.113 r_nbtor_other 0.09 r_xyhbond_nbd_other 0.073 r_chiral_restr 0.063 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19677 Nucleic Acid Atoms Solvent Atoms 754 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing SHARP phasing