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Y351F mutant of pentaerythritol tetranitrate reductase containing a bound acetate 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 2.19 43.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.685 α = 90 b = 68.838 β = 90 c = 88.915 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 2008-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.970 ESRF ID14-4
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 1.19 37.4 99.3 0.077 10.6 3.8 111179 111179
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) 1.19 1.23 99.7 0.248 4.4
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 1.19 7.98 110924 5564 99.5 0.1302 0.1293 0.1268 0.1467 0.1439 RANDOM 13.1949
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.523 r_dihedral_angle_4_deg 15.308 r_dihedral_angle_3_deg 11.936 r_dihedral_angle_1_deg 5.67 r_sphericity_free 4.571 r_sphericity_bonded 3.488 r_scangle_it 3.012 r_scbond_it 2.118 r_mcangle_it 1.545 r_angle_refined_deg 1.381
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.523 r_dihedral_angle_4_deg 15.308 r_dihedral_angle_3_deg 11.936 r_dihedral_angle_1_deg 5.67 r_sphericity_free 4.571 r_sphericity_bonded 3.488 r_scangle_it 3.012 r_scbond_it 2.118 r_mcangle_it 1.545 r_angle_refined_deg 1.381 r_angle_other_deg 1.379 r_mcbond_it 1.202 r_rigid_bond_restr 1.095 r_mcbond_other 0.867 r_symmetry_vdw_other 0.294 r_symmetry_hbond_refined 0.261 r_symmetry_vdw_refined 0.244 r_nbd_other 0.224 r_nbd_refined 0.211 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.082 r_nbtor_other 0.077 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 2758 Nucleic Acid Atoms Solvent Atoms 774 Heterogen Atoms 35
Software Software Software Name Purpose d*TREK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection d*TREK data reduction