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Pentaerythritol tetranitrate reductase co-crystal structure containing a bound (E)-1-(4'-hydroxyphenyl)-2-nitroethene molecule
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, SITTING DROP 6.2 293 100mM sodium cacodylate, 100 mM sodium acetate, 16-18% isopropanol, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.29 46.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.614 α = 90 b = 70.554 β = 90 c = 89.132 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 Q315 2009-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
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 55.32 98.3 0.059 0.059 20.6 5.3 111935 111935
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 0.121 0.121 5.4 5.3 16438
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 20.8 111853 5609 98.21 0.1217 0.1207 0.1181 0.1404 0.1368 RANDOM 10.8175
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.253 r_dihedral_angle_4_deg 12.076 r_dihedral_angle_3_deg 11.523 r_dihedral_angle_1_deg 5.85 r_sphericity_free 4.122 r_scangle_it 2.46 r_sphericity_bonded 1.986 r_scbond_it 1.846 r_angle_refined_deg 1.33 r_mcangle_it 1.286
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.253 r_dihedral_angle_4_deg 12.076 r_dihedral_angle_3_deg 11.523 r_dihedral_angle_1_deg 5.85 r_sphericity_free 4.122 r_scangle_it 2.46 r_sphericity_bonded 1.986 r_scbond_it 1.846 r_angle_refined_deg 1.33 r_mcangle_it 1.286 r_mcbond_it 1.103 r_rigid_bond_restr 1.014 r_angle_other_deg 0.906 r_mcbond_other 0.303 r_symmetry_vdw_other 0.231 r_nbd_refined 0.215 r_nbd_other 0.213 r_symmetry_hbond_refined 0.185 r_nbtor_refined 0.177 r_symmetry_vdw_refined 0.14 r_xyhbond_nbd_refined 0.119 r_nbtor_other 0.084 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2765 Nucleic Acid Atoms Solvent Atoms 779 Heterogen Atoms 43
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection