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Structure of S-nitrosoglutathione reductase from tomato (Solanum lycopersicum) crystallized in presence of NADH and glutathione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MC5 PDB ENTRY 1MC5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M MES pH 6.5, 13% PEG 20000, 4% glycerol (plus 2.5 mM NADH and 5 mM glutathione in the drop), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.64 α = 90 b = 78.04 β = 90 c = 124.26 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 PIXEL PSI PILATUS 6M 2011-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.98011 SOLEIL PROXIMA 1
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 2.1 28.8 99.3 0.124 9.21 44412 44113 2 1 28.59
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 2.1 2.22 97.3 0.757 1.83
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1MC5 2.1 28.79 44412 44055 2203 99.7 0.1841 0.1811 0.1883 0.2428 0.2529 RANDOM 31.19
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] 6.574 -9.112 2.538
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.86 t_omega_torsion 3.34 t_angle_deg 1.14 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.86 t_omega_torsion 3.34 t_angle_deg 1.14 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5698 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 122
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing BUSTER refinement XDS data reduction XDS data scaling