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Crystal structure of dialkylglycine decarboxylases bound with calcium ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DKA PDB entry 1DKA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 PEG4K, MES, PLP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.44 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.553 α = 90 b = 150.553 β = 90 c = 84.703 γ = 120
Symmetry Space Group P 64 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 100 CCD BRUKER 2004-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER
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 2.75 50 93.7 15215 14258 2 2
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 2.75 2.88 93.7
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 PDB entry 1DKA 2.75 30 2 15205 14257 725 0.219 0.2212 0.277 0.22 random
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]
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.3 c_bond_d 0.007 o_bond_d_na o_bond_d_prot o_angle_d o_angle_d_na o_angle_d_prot o_angle_deg_na o_angle_deg_prot o_dihedral_angle_d
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.3 c_bond_d 0.007 o_bond_d_na o_bond_d_prot o_angle_d o_angle_d_na o_angle_d_prot o_angle_deg_na o_angle_deg_prot o_dihedral_angle_d o_dihedral_angle_d_na o_dihedral_angle_d_prot o_improper_angle_d o_improper_angle_d_na o_improper_angle_d_prot o_mcbond_it o_mcangle_it o_scbond_it o_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3252 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 29
Software Software Software Name Purpose PROTEUM PLUS data collection PROTEUM PLUS data reduction CNS refinement PROTEUM PLUS data scaling CNS phasing