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Crystal structure of D-serine dehydratase from chicken kidney (EDTA treated)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ANU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOUR DIFFUSION, HANGING DROP, MICRO-SEEDING 6.5 293 12-15% PEG 4000, 50mM MES-NaOH, 10% 2-propanol, pH 6.5, VAPOUR DIFFUSION, HANGING DROP, MICRO-SEEDING, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.81 56.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.329 α = 90 b = 105.329 β = 90 c = 82.018 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 2011-03-06 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 2.8 90 99.9 12.6 6.9 11900 11883
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 2.8 2.95 99.7 6.7 1675
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3ANU 2.8 20 11245 11245 592 100 0.21293 0.21293 0.21065 0.2065 0.25677 0.2523 RANDOM 24.024
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] -0.65 -0.65 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.72 r_dihedral_angle_4_deg 17.202 r_dihedral_angle_3_deg 17.08 r_dihedral_angle_1_deg 6.126 r_scangle_it 2.598 r_scbond_it 1.483 r_angle_refined_deg 1.433 r_mcangle_it 1.136 r_mcbond_it 0.602 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.72 r_dihedral_angle_4_deg 17.202 r_dihedral_angle_3_deg 17.08 r_dihedral_angle_1_deg 6.126 r_scangle_it 2.598 r_scbond_it 1.483 r_angle_refined_deg 1.433 r_mcangle_it 1.136 r_mcbond_it 0.602 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2767 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 15
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling