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Bifunctional LysX/ArgX from Thermococcus kodakarensis with LysW-gamma-AAA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VPD 3VPD, 3WWL experimental model PDB 3WWL 3VPD, 3WWL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 MPD, PEG 3350, Imidazole pH 6.5, Ammonium sulfate, AMP-PNP, AAA, MgSO4
Crystal Properties Matthews coefficient Solvent content 2.5 50.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.15 α = 90 b = 135.099 β = 97.49 c = 136.977 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 270 2014-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1 Photon Factory AR-NE3A
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 2.18 50 99.7 0.087 6.5 3.8 142143
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 2.18 2.22 100 0.388 3.8
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 3VPD, 3WWL 2.18 50 134987 7130 99.2 0.182 0.18 0.1896 0.22 0.2257 RANDOM 53.42
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] 0.18 -0.01 -0.08 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.902 r_dihedral_angle_3_deg 16.749 r_dihedral_angle_4_deg 14.097 r_dihedral_angle_1_deg 6.135 r_mcangle_it 2.736 r_mcbond_it 1.782 r_mcbond_other 1.782 r_angle_refined_deg 1.383 r_angle_other_deg 0.789 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.902 r_dihedral_angle_3_deg 16.749 r_dihedral_angle_4_deg 14.097 r_dihedral_angle_1_deg 6.135 r_mcangle_it 2.736 r_mcbond_it 1.782 r_mcbond_other 1.782 r_angle_refined_deg 1.383 r_angle_other_deg 0.789 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18615 Nucleic Acid Atoms Solvent Atoms 628 Heterogen Atoms 273
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction PHASER phasing