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Y351A 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 45.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.427 α = 90 b = 70.329 β = 90 c = 88.876 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 0.9696 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 1.1 30 92.4 0.043 21.9 4 135417 135417
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.1 1.14 97.7 15.3 3.76
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 1.1 21.08 135251 6775 92.57 0.1247 0.1239 0.121 0.1402 0.1368 RANDOM 7.8628
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 39.561 r_dihedral_angle_4_deg 12.517 r_dihedral_angle_3_deg 12.343 r_dihedral_angle_1_deg 5.95 r_sphericity_free 3.773 r_scangle_it 2.411 r_angle_other_deg 2.229 r_sphericity_bonded 1.771 r_scbond_it 1.736 r_angle_refined_deg 1.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.561 r_dihedral_angle_4_deg 12.517 r_dihedral_angle_3_deg 12.343 r_dihedral_angle_1_deg 5.95 r_sphericity_free 3.773 r_scangle_it 2.411 r_angle_other_deg 2.229 r_sphericity_bonded 1.771 r_scbond_it 1.736 r_angle_refined_deg 1.325 r_mcangle_it 1.25 r_mcbond_it 1.079 r_rigid_bond_restr 0.958 r_mcbond_other 0.642 r_nbd_refined 0.417 r_symmetry_vdw_other 0.374 r_symmetry_vdw_refined 0.342 r_nbd_other 0.303 r_nbtor_refined 0.183 r_symmetry_hbond_refined 0.182 r_nbtor_other 0.115 r_xyhbond_nbd_refined 0.085 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2758 Nucleic Acid Atoms Solvent Atoms 628 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