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Crystal structure of LysY from Thermus thermophilus complexed with NADP+ and LysW-gamma-aminoadipic semialdehyde
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OZP 2OZP, 3WWL experimental model PDB 3WWL 2OZP, 3WWL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 PEG 2000 MME, calcium acetate, NADP, HEPES-NaOH
Crystal Properties Matthews coefficient Solvent content 2.07 40.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.53 α = 90 b = 83.53 β = 90 c = 168.321 γ = 120
Symmetry Space Group P 32 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 2014-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.8 50 99.4 0.112 27.8 5.5 64110
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 1.8 1.83 100 0.49 2.8 5.7
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 2OZP, 3WWL 1.8 36.37 60465 3226 99.42 0.17001 0.1678 0.1795 0.21284 0.2208 RANDOM 32.617
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.682 r_dihedral_angle_4_deg 16.178 r_dihedral_angle_3_deg 14.24 r_dihedral_angle_1_deg 6.058 r_long_range_B_other 5.41 r_long_range_B_refined 5.409 r_scangle_other 3.714 r_mcangle_it 2.776 r_mcangle_other 2.775 r_scbond_it 2.358
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.682 r_dihedral_angle_4_deg 16.178 r_dihedral_angle_3_deg 14.24 r_dihedral_angle_1_deg 6.058 r_long_range_B_other 5.41 r_long_range_B_refined 5.409 r_scangle_other 3.714 r_mcangle_it 2.776 r_mcangle_other 2.775 r_scbond_it 2.358 r_scbond_other 2.358 r_mcbond_it 1.871 r_mcbond_other 1.863 r_angle_refined_deg 1.488 r_angle_other_deg 0.784 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5703 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement Coot model building HKL-2000 data scaling HKL-2000 data collection PHASER phasing