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HePTP Catalytic Domain (residues 44-339), S225D mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZC0 PDB Entry 1ZC0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 277 K/Na Phosphate, Ammonium Acetate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.23 70.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.52 α = 90 b = 127.52 β = 90 c = 60.133 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2005-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.54
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 2.05 50 96.3 0.089 9.9 3.1 33843 33843 1 1
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 2.05 2.12 82.5 82.5 0.456 1.8
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 (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB Entry 1ZC0 2.05 20 33803 33803 1689 96.32 0.179 0.179 0.178 0.1754 0.206 0.2012 RANDOM 32.403
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] 0.07 0.03 0.07 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.151 r_dihedral_angle_4_deg 17.625 r_dihedral_angle_3_deg 13.484 r_dihedral_angle_1_deg 6.737 r_scangle_it 3.646 r_scbond_it 2.377 r_mcangle_it 1.745 r_angle_refined_deg 1.588 r_mcbond_it 1.089 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.151 r_dihedral_angle_4_deg 17.625 r_dihedral_angle_3_deg 13.484 r_dihedral_angle_1_deg 6.737 r_scangle_it 3.646 r_scbond_it 2.377 r_mcangle_it 1.745 r_angle_refined_deg 1.588 r_mcbond_it 1.089 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.277 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.192 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.099 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2267 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 11
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction