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Y351S 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 2.28 46.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.49 α = 90 b = 70.309 β = 90 c = 88.971 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 29.99 93.6 0.051 14.9 3.62 181871
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 1.04 85.4 0.192 3.9 1.82 16399
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 17.8 181855 9174 93.62 0.1347 0.1341 0.1333 0.1476 0.1462 RANDOM 9.8627
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 40.159 r_dihedral_angle_4_deg 12.899 r_dihedral_angle_3_deg 12.156 r_dihedral_angle_1_deg 5.93 r_sphericity_free 3.589 r_scangle_it 2.234 r_sphericity_bonded 1.923 r_scbond_it 1.641 r_angle_refined_deg 1.406 r_mcangle_it 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.159 r_dihedral_angle_4_deg 12.899 r_dihedral_angle_3_deg 12.156 r_dihedral_angle_1_deg 5.93 r_sphericity_free 3.589 r_scangle_it 2.234 r_sphericity_bonded 1.923 r_scbond_it 1.641 r_angle_refined_deg 1.406 r_mcangle_it 1.23 r_angle_other_deg 0.93 r_mcbond_it 0.914 r_rigid_bond_restr 0.738 r_nbd_refined 0.517 r_mcbond_other 0.32 r_symmetry_vdw_other 0.295 r_symmetry_vdw_refined 0.262 r_nbd_other 0.259 r_symmetry_hbond_refined 0.192 r_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.182 r_chiral_restr 0.121 r_nbtor_other 0.112 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2759 Nucleic Acid Atoms Solvent Atoms 768 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