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Crystal structure of LysZ from Thermus thermophilus complex with LysW
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WWL PDB ENTRIES 3WWL and 3U6U experimental model PDB 3U6U PDB ENTRIES 3WWL and 3U6U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 20% (v/w) PEG 8000, 0.1M MES pH 6.0, 0.2M Calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 52.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.809 α = 90 b = 69.809 β = 90 c = 148.036 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315r 2009-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
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 1.85 50 99.8 0.067 46.9 14 32240 32177 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 100 0.72 3.6 14.2 1582
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRIES 3WWL and 3U6U 1.85 28.77 32240 30470 1626 99.76 0.17876 0.17695 0.21282 0.214 RANDOM 35.605
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 32.145 r_dihedral_angle_4_deg 16.935 r_dihedral_angle_3_deg 14.454 r_long_range_B_refined 6.869 r_long_range_B_other 6.67 r_dihedral_angle_1_deg 6.018 r_scangle_other 3.698 r_mcangle_it 2.415 r_mcangle_other 2.415 r_scbond_it 2.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.145 r_dihedral_angle_4_deg 16.935 r_dihedral_angle_3_deg 14.454 r_long_range_B_refined 6.869 r_long_range_B_other 6.67 r_dihedral_angle_1_deg 6.018 r_scangle_other 3.698 r_mcangle_it 2.415 r_mcangle_other 2.415 r_scbond_it 2.266 r_scbond_other 2.265 r_mcbond_it 1.524 r_mcbond_other 1.523 r_angle_refined_deg 1.314 r_angle_other_deg 0.788 r_chiral_restr 0.084 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2400 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 6
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling