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Crystal structure of a fragment (residues 11 to 161) of L-serine dehydratase from Legionella pneumophila
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 0.2 Ammonium sulphate, 0.1M BisTris pH 6.5, 25% Peg 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.52 65.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.319 α = 90 b = 76.835 β = 90 c = 108.135 γ = 90
Symmetry Space Group I 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315 2006-08-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9793, 0.97943 APS 19-ID
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 2.05 40 99.1 0.078 17 7.1 15069 14934
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 2.05 2.09 100 0.478 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.05 40 14930 14168 756 99.04 0.19602 0.19455 0.2 0.22418 0.2323 RANDOM 38.101
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] -0.58 -0.07 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.306 r_dihedral_angle_4_deg 29.645 r_dihedral_angle_3_deg 16.31 r_dihedral_angle_1_deg 11.653 r_scangle_it 4.392 r_scbond_it 2.886 r_angle_refined_deg 2.009 r_mcangle_it 1.996 r_mcbond_it 1.389 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.306 r_dihedral_angle_4_deg 29.645 r_dihedral_angle_3_deg 16.31 r_dihedral_angle_1_deg 11.653 r_scangle_it 4.392 r_scbond_it 2.886 r_angle_refined_deg 2.009 r_mcangle_it 1.996 r_mcbond_it 1.389 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.24 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.228 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.156 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1095 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building