☰ Navigation Tabs
Crystal structure of holo D-serine dehydratase from Escherichia coli at 1.55 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 0.7 M sodium citrate, 0.1 M imidazole/maleate buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.67 53.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.774 α = 90 b = 47.806 β = 104.96 c = 75.193 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 MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 0.979 SRS PX10.1
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 1.55 72.74 0.085 15.9 4.7 73947 2 15.8
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 1.55 1.61 0.41 2.25 2.5
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 MOLECULAR REPLACEMENT THROUGHOUT 1.55 50 70687 3546 95.59 0.161 0.1592 0.1569 0.1939 0.1915 RANDOM 16.9927
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] -0.36 0.19 0.25 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.805 r_dihedral_angle_4_deg 14.08 r_dihedral_angle_3_deg 12.761 r_dihedral_angle_1_deg 5.351 r_scangle_it 3.765 r_scbond_it 2.466 r_angle_refined_deg 1.524 r_mcangle_it 1.503 r_mcbond_it 0.9 r_metal_ion_refined 0.378
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.805 r_dihedral_angle_4_deg 14.08 r_dihedral_angle_3_deg 12.761 r_dihedral_angle_1_deg 5.351 r_scangle_it 3.765 r_scbond_it 2.466 r_angle_refined_deg 1.524 r_mcangle_it 1.503 r_mcbond_it 0.9 r_metal_ion_refined 0.378 r_nbtor_refined 0.313 r_nbd_refined 0.24 r_symmetry_vdw_refined 0.218 r_symmetry_hbond_refined 0.217 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3324 Nucleic Acid Atoms Solvent Atoms 668 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing