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Pentaerythritol tetranitrate reductase co-crystal structure with bound (E)-1-(2'-hydroxyphenyl)-2-nitroethene
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H50
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.2 293 100mM sodium cacodylate, 100 mM sodium acetate, 16-18% isopropanol, pH 6.2, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 45.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.533 α = 90 b = 70.349 β = 90 c = 88.948 γ = 90
Symmetry Space Group P 21 21 21
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 1 2010-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 1.07 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.2 55.216 99.5 0.098 0.098 12.2 4.4 112611 112611
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.2 1.26 100 0.274 0.274 2.6 4.5 16325
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 1H50 1.2 30.02 112529 5645 99.39 0.126 0.1248 0.1227 0.1475 0.1429 RANDOM 9.8403
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] 0.01 0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.889 r_dihedral_angle_4_deg 12.592 r_dihedral_angle_3_deg 11.865 r_dihedral_angle_1_deg 5.896 r_sphericity_free 4.054 r_scangle_it 2.448 r_scbond_it 1.821 r_sphericity_bonded 1.786 r_angle_refined_deg 1.364 r_mcangle_it 1.286
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.889 r_dihedral_angle_4_deg 12.592 r_dihedral_angle_3_deg 11.865 r_dihedral_angle_1_deg 5.896 r_sphericity_free 4.054 r_scangle_it 2.448 r_scbond_it 1.821 r_sphericity_bonded 1.786 r_angle_refined_deg 1.364 r_mcangle_it 1.286 r_mcbond_it 0.989 r_angle_other_deg 0.944 r_rigid_bond_restr 0.849 r_mcbond_other 0.362 r_symmetry_vdw_other 0.296 r_symmetry_vdw_refined 0.249 r_symmetry_hbond_refined 0.223 r_nbd_refined 0.212 r_nbd_other 0.209 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.112 r_nbtor_other 0.084 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2765 Nucleic Acid Atoms Solvent Atoms 745 Heterogen Atoms 43
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection