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GTA mutant with mercury - E303D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LZ0 PDB ENTRY 1LZ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 10 ul drops with 6-8 mg/ml protein, 70 mM N-(2-acetamido)-2-iminodiacetic acid (ADA) pH 7.5, 50 mM, sodium acetate pH 4.6, 40 mM NaCl, 5-8 mM MnCl2, 2.5% (v/v) 2-methyl-2,4-pentanediol (MPD), 5%(v/v) glycerol, 2%(w/v) PEG 4000, and 0.3-0.5 mM 3-chloromercuri-2-methoxypropylurea suspended over 1 ml of a resevoir solution: 50 mM ADA pH 7.5, 10 mM MnCl2, 100 mM ammonium sulfate, 5%(v/v) MPD, 10%(v/v) glycerol, and 8-10%(w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.27 45.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.77 α = 90 b = 148.83 β = 90 c = 79.34 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 IMAGE PLATE RIGAKU RAXIS IV++ 2011-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.61 74.33 98.9 0.042 17.8 4.27 40426
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 1.61 1.67 95.7 0.27 3.4 3.27 3849
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 PDB ENTRY 1LZ0 1.61 74.33 38400 2026 98.81 0.188 0.1868 0.1983 0.2105 0.22 RANDOM 26.131
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 -0.11 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.91 r_dihedral_angle_4_deg 21.351 r_dihedral_angle_3_deg 12.879 r_dihedral_angle_1_deg 6.377 r_mcangle_it 2.519 r_mcbond_it 1.731 r_mcbond_other 1.73 r_angle_refined_deg 1.601 r_angle_other_deg 0.822 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.91 r_dihedral_angle_4_deg 21.351 r_dihedral_angle_3_deg 12.879 r_dihedral_angle_1_deg 6.377 r_mcangle_it 2.519 r_mcbond_it 1.731 r_mcbond_other 1.73 r_angle_refined_deg 1.601 r_angle_other_deg 0.822 r_chiral_restr 0.101 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2117 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 4
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction MOLREP phasing