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Pentaerythritol tetranitrate reductase co-crystal structure containing bound (E)-1-(3'-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 46.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.494 α = 90 b = 70.642 β = 90 c = 88.956 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 2010-03-22 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 98.6 0.04 0.04 18.8 3.4 111905 111905
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 99.2 0.172 0.172 4.1 3.3 16255
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 21.21 111821 5606 98.43 0.1319 0.1307 0.1279 0.1548 0.1494 RANDOM 11.8041
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 41.081 r_dihedral_angle_4_deg 12.676 r_dihedral_angle_3_deg 12.195 r_dihedral_angle_1_deg 5.901 r_sphericity_free 5.287 r_sphericity_bonded 2.888 r_scangle_it 2.875 r_scbond_it 2.111 r_mcangle_it 1.523 r_angle_refined_deg 1.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.081 r_dihedral_angle_4_deg 12.676 r_dihedral_angle_3_deg 12.195 r_dihedral_angle_1_deg 5.901 r_sphericity_free 5.287 r_sphericity_bonded 2.888 r_scangle_it 2.875 r_scbond_it 2.111 r_mcangle_it 1.523 r_angle_refined_deg 1.409 r_angle_other_deg 1.363 r_mcbond_it 1.206 r_rigid_bond_restr 1.164 r_mcbond_other 0.747 r_symmetry_vdw_other 0.297 r_symmetry_vdw_refined 0.229 r_nbd_other 0.222 r_nbd_refined 0.211 r_nbtor_refined 0.18 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.083 r_nbtor_other 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2769 Nucleic Acid Atoms Solvent Atoms 708 Heterogen Atoms 55
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection