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Crystal structure of D-serine dehydratase in complex with D-serine from chicken kidney (EDTA-treated)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP, MICRO-SEEDING 6.5 293 12-15% PEG 4000, 50mM MES-NaOH, 10% 2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, MICRO-SEEDING, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.79 55.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.053 α = 90 b = 105.053 β = 90 c = 81.916 γ = 90
Symmetry Space Group P 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 270 2011-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.65 100 99.9 13865 13850
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.79 99.9 7.04 1924
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 (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 MOLECULAR REPLACEMENT THROUGHOUT 2.65 20 13118 13118 690 100 0.20928 0.20928 0.20623 0.2032 0.26607 0.2601 RANDOM 25.87
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] -0.89 -0.89 1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.812 r_dihedral_angle_4_deg 18.41 r_dihedral_angle_3_deg 17.614 r_dihedral_angle_1_deg 5.839 r_scangle_it 2.298 r_scbond_it 1.345 r_angle_refined_deg 1.288 r_mcangle_it 1.075 r_mcbond_it 0.573 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.812 r_dihedral_angle_4_deg 18.41 r_dihedral_angle_3_deg 17.614 r_dihedral_angle_1_deg 5.839 r_scangle_it 2.298 r_scbond_it 1.345 r_angle_refined_deg 1.288 r_mcangle_it 1.075 r_mcbond_it 0.573 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2772 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 22
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling