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X-ray crystal structure of arginine decarboxylase complexed with Arginine from Vibrio vulnificus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1 M HEPES pH 7.0, 0.2 M MgCl2, 12% PEG 4000., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.49 50.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.648 α = 90 b = 119.365 β = 96.3 c = 121.84 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 315 2009-02-20 M SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97935 APS 19-ID
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 2.3 121.1 98.8 0.127 17.4 4.6 128263 127349 2.3 2.1
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 2.3 2.34 100 0.888 2.1 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 SAD THROUGHOUT 2.3 121.1 2.1 128263 127349 6366 98.75 0.1962 0.18182 0.17878 0.1789 0.23921 0.2372 RANDOM 28.874
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] 0.07 1.9 -0.49 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.327 r_dihedral_angle_3_deg 18.219 r_dihedral_angle_4_deg 17.203 r_dihedral_angle_1_deg 6.756 r_scangle_it 5.421 r_scbond_it 3.494 r_mcangle_it 2.007 r_angle_refined_deg 1.831 r_mcbond_it 1.032 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.327 r_dihedral_angle_3_deg 18.219 r_dihedral_angle_4_deg 17.203 r_dihedral_angle_1_deg 6.756 r_scangle_it 5.421 r_scbond_it 3.494 r_mcangle_it 2.007 r_angle_refined_deg 1.831 r_mcbond_it 1.032 r_chiral_restr 0.122 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20053 Nucleic Acid Atoms Solvent Atoms 443 Heterogen Atoms 96
Software Software Software Name Purpose HKL-3000 data collection SHELXD phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling