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T26S 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 PDB ENTRY 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 2.15 42.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.919 α = 90 b = 69.063 β = 90 c = 88.871 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++ 2008-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.542
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 1.5 54.554 99.8 0.054 0.054 19.6 4.5 56705 56705
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.58 100 0.164 0.164 0.188 0.089 4.3 4.3 8161
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 1H50 1.5 16.35 56644 2872 99.87 0.147 0.1458 0.1549 0.1706 0.1808 RANDOM 14.5332
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.756 r_dihedral_angle_4_deg 15.243 r_dihedral_angle_3_deg 12.626 r_dihedral_angle_1_deg 5.471 r_sphericity_free 3.262 r_scangle_it 2.238 r_scbond_it 1.658 r_sphericity_bonded 1.385 r_angle_refined_deg 1.212 r_mcangle_it 1.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.756 r_dihedral_angle_4_deg 15.243 r_dihedral_angle_3_deg 12.626 r_dihedral_angle_1_deg 5.471 r_sphericity_free 3.262 r_scangle_it 2.238 r_scbond_it 1.658 r_sphericity_bonded 1.385 r_angle_refined_deg 1.212 r_mcangle_it 1.076 r_angle_other_deg 0.976 r_rigid_bond_restr 0.897 r_mcbond_it 0.775 r_mcbond_other 0.303 r_symmetry_vdw_other 0.271 r_nbd_other 0.205 r_nbd_refined 0.204 r_nbtor_refined 0.176 r_symmetry_vdw_refined 0.166 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.109 r_nbtor_other 0.083 r_chiral_restr 0.072 r_bond_other_d 0.008 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2756 Nucleic Acid Atoms Solvent Atoms 675 Heterogen Atoms 35
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction