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Crystal structure of Lysine decarboxylase from Selenomonas ruminantium in C2 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PLJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 Sodium citrate, Sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.59 52.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.45 α = 90 b = 70.794 β = 101.03 c = 88.061 γ = 90
Symmetry Space Group C 1 2 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 270 2014-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
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 2.9 50 95.2 0.145 17.2 3.5 18678
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.95 94.2 0.346 0.67 3.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2PLJ 2.91 50 17748 930 94.68 0.18125 0.17716 0.23364 0.2164 RANDOM 21.219
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] -1.29 0.3 3.2 -1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.094 r_dihedral_angle_3_deg 18.497 r_dihedral_angle_4_deg 17.266 r_dihedral_angle_1_deg 7.299 r_long_range_B_refined 4.501 r_long_range_B_other 4.501 r_mcangle_it 2.45 r_mcangle_other 2.45 r_scangle_other 2.403 r_angle_refined_deg 1.704
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.094 r_dihedral_angle_3_deg 18.497 r_dihedral_angle_4_deg 17.266 r_dihedral_angle_1_deg 7.299 r_long_range_B_refined 4.501 r_long_range_B_other 4.501 r_mcangle_it 2.45 r_mcangle_other 2.45 r_scangle_other 2.403 r_angle_refined_deg 1.704 r_scbond_it 1.38 r_scbond_other 1.38 r_mcbond_it 1.374 r_mcbond_other 1.374 r_angle_other_deg 1.024 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 5785 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling MOLREP phasing PDB_EXTRACT data extraction