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The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 PEG 2000, 2-methyl-2,4-pentanediol, glycerol, n-[2-hydroxyethyl]piperazine-N'-[2-ethanesulfonic acid], beta-octyl glucoside, putrescine, ethylenediaminetetraacetic acid, dithiothreitol, arginine methyl ester, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.97 37.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.46 α = 90 b = 92.88 β = 94.74 c = 87.11 γ = 90
Symmetry Space Group P 1 21 1
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 4 2002-01-01 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2002-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F2 0.980 CHESS F2 2 SYNCHROTRON APS BEAMLINE 8-BM 0.9793 APS 8-BM
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 1.4 29.16 59.9 0.063 11.2 2.7 105327 103325 11.4
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) 1.4 1.45 4.4 0.229 2.6 1.1 771
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 MOLECULAR REPLACEMENT THROUGHOUT 1.4 29.16 105327 101892 10235 57.9 0.196 0.1915 0.1915 0.1808 0.215 0.203 RANDOM 17.8
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] -3.81 -0.99 6.79 -2.9
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.9 c_scangle_it 3.18 c_mcangle_it 2.17 c_scbond_it 2.13 c_mcbond_it 1.44 c_angle_deg 1.3 c_improper_angle_d 1.16 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7406 Nucleic Acid Atoms Solvent Atoms 800 Heterogen Atoms 54
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing