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Crystal structure of LysZ from Thermus thermophilus with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3U6U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1.1M tri-sodium citrate, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.23 70.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.49 α = 90 b = 80.49 β = 90 c = 152.281 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 210 2010-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
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 2.8 50 100 0.049 59.8 14.2 13007 13002 -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 2.8 2.9 100 0.394 8.7 14.5 2355
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 3U6U 2.8 42.94 12318 628 99.9 0.18843 0.18657 0.1899 0.22546 0.2264 RANDOM 69.494
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] -0.56 -0.56 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.486 r_dihedral_angle_4_deg 16.768 r_dihedral_angle_3_deg 15.387 r_dihedral_angle_1_deg 5.674 r_long_range_B_refined 5.6 r_long_range_B_other 5.598 r_scangle_other 3.451 r_mcangle_it 2.468 r_mcangle_other 2.467 r_scbond_it 2.038
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.486 r_dihedral_angle_4_deg 16.768 r_dihedral_angle_3_deg 15.387 r_dihedral_angle_1_deg 5.674 r_long_range_B_refined 5.6 r_long_range_B_other 5.598 r_scangle_other 3.451 r_mcangle_it 2.468 r_mcangle_other 2.467 r_scbond_it 2.038 r_scbond_other 2.037 r_mcbond_it 1.472 r_mcbond_other 1.472 r_angle_refined_deg 1.191 r_angle_other_deg 0.693 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2048 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 27
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling