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Structure of Pentaerythritol tetranitrate reductase in complex with 1,4-androstadien-3,17-dione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OYA PDB ENTRY 1OYA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 PEG 3000, 0.1M CACODYLIC ACID, 15% MEOH PH 6.8
Crystal Properties Matthews coefficient Solvent content 2.3 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.709 α = 90 b = 69.013 β = 90 c = 88.708 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 IMAGE PLATE RIGAKU RAXIS IV IMAGE PLATE MIRRORS 2000-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.9 100 94.4 0.081 9.5 2.5 21069 19.9
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 1.9 1.97 94.6 0.35 5.5
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 PDB ENTRY 1OYA 1.9 100 25805 1223 91.7 0.194 0.194 0.1937 0.232 0.2294 RANDOM 24.6
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] -3.05 3.41 -0.37
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_angle_deg 1.3 c_improper_angle_d 0.83 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_angle_deg 1.3 c_improper_angle_d 0.83 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2778 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 52
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing