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Structure of Dialkylglycine Decarboxylase Complexed with 1-Aminocyclopentanephosphonate
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 6.4 15% PEG 4000, 0.2-0.4 M SODIUM PYRUVATE, 0.015 M MES-KOH (PH 6.4)
Crystal Properties Matthews coefficient Solvent content 3.01 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.29 α = 90 b = 151.29 β = 90 c = 84.79 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 IMAGE PLATE RIGAKU RAXIS IV 2001-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 30 96.1 0.077 18.9 3.21 28332 2 -2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.28 98.1 0.318 11.3 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1DKA 2.2 20 2 2 27846 1417 94.3 0.192 0.189 0.239 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 t_dihedral_angle_d 17.3 t_angle_deg 1.957 t_bond_d 0.027 t_gen_planes 0.02 o_bond_d_na o_bond_d_prot o_angle_d_na o_angle_d_prot o_angle_deg o_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation t_dihedral_angle_d 17.3 t_angle_deg 1.957 t_bond_d 0.027 t_gen_planes 0.02 o_bond_d_na o_bond_d_prot o_angle_d_na o_angle_d_prot o_angle_deg o_angle_deg_na o_angle_deg_prot 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 210 Heterogen Atoms 27
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement TNT refinement CNS phasing