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Crystal structure of D-serine dehydratase from chicken kidney
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 12-15% PEG 4000, 50mM MES-NaOH, 10% 2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.75 55.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.578 α = 90 b = 104.578 β = 90 c = 81.449 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 315r 2010-03-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000, 1.28179, 1.28284, 1.25510, 1.30300 Photon Factory BL-5A
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 1.9 17 99.2 26.5 6.9 36209 35919
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 1.9 2 99.7 3.5 6.7 5021
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 MAD THROUGHOUT 1.9 17 34123 34123 1796 100 0.19035 0.19035 0.18906 0.1989 0.21486 0.226 RANDOM 35.334
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] -1.4 -1.4 2.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.414 r_dihedral_angle_4_deg 16.255 r_dihedral_angle_3_deg 14.882 r_dihedral_angle_1_deg 5.873 r_scangle_it 3.108 r_scbond_it 1.894 r_angle_refined_deg 1.309 r_mcangle_it 1.176 r_mcbond_it 0.647 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.414 r_dihedral_angle_4_deg 16.255 r_dihedral_angle_3_deg 14.882 r_dihedral_angle_1_deg 5.873 r_scangle_it 3.108 r_scbond_it 1.894 r_angle_refined_deg 1.309 r_mcangle_it 1.176 r_mcbond_it 0.647 r_chiral_restr 0.096 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2778 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 17
Software Software Software Name Purpose ADSC data collection SHARP phasing REFMAC refinement XDS data reduction XSCALE data scaling