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Crystal Structure of 2,6-Dihydroxybenzoate Decarboxylase Complexed with 2,6-Dihydroxybenzoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 PEG 8000, HEPES-Na, Ethyleneglycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 50.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.071 α = 90 b = 113.611 β = 90 c = 119.102 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315 2005-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 40.226 100 116818 116804 14.2
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 1.9 1.97 100
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 (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 2DVT 1.9 40.22 116818 116804 11691 99.8 0.176 0.176 0.1756 0.206 0.2057 RANDOM 20.5
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] 1.1 -0.54 -0.56
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_scbond_it 17.1 c_scangle_it 11.62 c_mcangle_it 1.46 c_angle_deg 1.3 c_mcbond_it 1.05 c_improper_angle_d 0.82 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10460 Nucleic Acid Atoms Solvent Atoms 1034 Heterogen Atoms 48
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing