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wild type human PrxV with DTT bound as a competitive inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HD2 pdb code 1HD2 with benzoate removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 Reservoir contained 1.6 M ammonium sulfate, 0.1 M sodium citrate, 0.2 M sodium/potassium tartrate. Protein was stored at 0.8 mM with 10 mM DTT., pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.83 67.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.313 α = 90 b = 67.313 β = 90 c = 123.867 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 100 CCD ADSC QUANTUM 210 2009-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.978 ALS 5.0.1
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 1.45 59 99.98 0.094 30.9 36.7 48609
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) 1.45 1.53 100 0.393 6.9 14 7365
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 Rigid body refinement of starting model THROUGHOUT pdb code 1HD2 with benzoate removed 1.45 59 48609 2633 99.98 0.11422 0.11303 0.1082 0.13618 0.1287 RANDOM 11.049
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] -0.29 -0.29 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.523 r_dihedral_angle_4_deg 11.064 r_dihedral_angle_3_deg 10.911 r_scangle_it 9.969 r_scbond_it 6.9 r_dihedral_angle_1_deg 6.104 r_mcangle_it 4.357 r_mcbond_it 3.104 r_rigid_bond_restr 2.816 r_angle_refined_deg 2.726
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.523 r_dihedral_angle_4_deg 11.064 r_dihedral_angle_3_deg 10.911 r_scangle_it 9.969 r_scbond_it 6.9 r_dihedral_angle_1_deg 6.104 r_mcangle_it 4.357 r_mcbond_it 3.104 r_rigid_bond_restr 2.816 r_angle_refined_deg 2.726 r_angle_other_deg 2.413 r_mcbond_other 1.081 r_chiral_restr 0.161 r_gen_planes_refined 0.013 r_bond_refined_d 0.012 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1190 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing