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Crystal structure of Selenomethionine incorporated apo D-serine deaminase from Salmonella tyhimurium
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 298 0.1M Trisodium citrate pH 6.1, 0.4M Ammonium sulphatem, 0.8M Lithium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.52 51.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.46 α = 90 b = 188.39 β = 90 c = 46.59 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 225 mm CCD 2009-10-28 M MAD 2 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2009-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97848, 0.97872, 1.01876, 0.97083 ESRF BM14 2 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 1.93 48.4 93.7 0.053 28.2 9.1 36067 14.7
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 1.9 2 82.5 0.174 12 10.1 4560
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 1.93 36.17 34192 1822 94.37 0.18212 0.18063 0.1823 0.20986 0.2121 RANDOM 15.799
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.541 r_dihedral_angle_4_deg 15.155 r_dihedral_angle_3_deg 12.638 r_dihedral_angle_1_deg 4.8 r_scangle_it 1.332 r_angle_refined_deg 0.915 r_scbond_it 0.83 r_mcangle_it 0.565 r_mcbond_it 0.294 r_chiral_restr 0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.541 r_dihedral_angle_4_deg 15.155 r_dihedral_angle_3_deg 12.638 r_dihedral_angle_1_deg 4.8 r_scangle_it 1.332 r_angle_refined_deg 0.915 r_scbond_it 0.83 r_mcangle_it 0.565 r_mcbond_it 0.294 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 3291 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 36
Software Software Software Name Purpose MAR345dtb data collection Auto-Rickshaw phasing REFMAC refinement MOSFLM data reduction SCALA data scaling