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Crystal structure of glycerol trinitrate reductase NerA from Agrobacterium radiobacter in complex with 1-nitro-2-phenylpropene
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JIC PDB entry 4jic
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6 293 0.2 M ammonium sulfate, 0.1 M BIS-TRIS, 25% w/v polyethylene glycol 3,350, pH 6.0, Microbatch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.15 α = 90 b = 69.98 β = 90 c = 91.99 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 MARMOSAIC 225 mm CCD 2010-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.49 55.69 99.8 14144 14125
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.49 2.62 99.8 0.677 3.5 2021
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB entry 4jic 2.49 50.343 1.33 14144 14091 703 99.77 0.2159 0.2135 0.2005 0.2625 0.239 RANDOM
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] -3.3128 2.7321 5.3558
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.177 f_angle_d 0.739 f_chiral_restr 0.054 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2790 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 51
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing PHENIX refinement MOSFLM data reduction SCALA data scaling