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Crystal structure of Arginine decarboxylase (AdiA) from Salmonella typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VYC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8 298 2.0M NaCl and 10% PEG8000, Tris pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.87 57.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.36 α = 90 b = 193.25 β = 90 c = 280.16 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 MAR CCD 165 mm 2010-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97625 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) CC (Half) 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 3.1 57.12 91.2 0.26 0.278 0.095 0.972 7.2 8 160279 16.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.27 83.4 0.72 0.77 0.267 0.799 2.7 7.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2VYC 3.1 57.12 152238 7890 90.82 0.24213 0.2406 0.2386 0.27179 0.2706 RANDOM 28.251
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] 0.23 0.18 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.722 r_dihedral_angle_3_deg 17.561 r_dihedral_angle_4_deg 13.481 r_dihedral_angle_1_deg 5.471 r_long_range_B_refined 2.972 r_long_range_B_other 2.967 r_mcangle_it 1.005 r_mcangle_other 1.005 r_angle_refined_deg 0.935 r_angle_other_deg 0.788
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.722 r_dihedral_angle_3_deg 17.561 r_dihedral_angle_4_deg 13.481 r_dihedral_angle_1_deg 5.471 r_long_range_B_refined 2.972 r_long_range_B_other 2.967 r_mcangle_it 1.005 r_mcangle_other 1.005 r_angle_refined_deg 0.935 r_angle_other_deg 0.788 r_scangle_other 0.716 r_mcbond_it 0.543 r_mcbond_other 0.543 r_scbond_it 0.377 r_scbond_other 0.375 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_bond_other_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 56095 Nucleic Acid Atoms Solvent Atoms 1385 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing