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Crystal Structure of partially reduced Periplasmic Nitrate Reductase from Cupriavidus necator using Ionic Liquids
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NAP PDB ENTRY 2NAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 15% PEG 3350, 0.2M sodium formate, 0.4M [C4MIM]Cl-, pH 7.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.4 α = 90 b = 71.41 β = 121.04 c = 128.41 γ = 90
Symmetry Space Group C 1 2 1
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 4 2007-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 1.72 28.34 99.6174 3.5 130188 97895 4 935
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 1.72 1.81 99.6174
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 (All) 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 2NAP 1.72 27.63 154350 93004 4889 99.62 0.1435 0.14473 0.14278 0.1422 0.1815 0.1803 RANDOM 12.375
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] -0.09 -0.04 0.07 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.44 r_dihedral_angle_4_deg 18.611 r_dihedral_angle_3_deg 13.8 r_dihedral_angle_1_deg 8.731 r_scangle_it 4.383 r_scbond_it 2.971 r_angle_refined_deg 2.31 r_mcangle_it 1.936 r_mcbond_it 1.289 r_chiral_restr 0.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.44 r_dihedral_angle_4_deg 18.611 r_dihedral_angle_3_deg 13.8 r_dihedral_angle_1_deg 8.731 r_scangle_it 4.383 r_scbond_it 2.971 r_angle_refined_deg 2.31 r_mcangle_it 1.936 r_mcbond_it 1.289 r_chiral_restr 0.198 r_bond_refined_d 0.028 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7121 Nucleic Acid Atoms Solvent Atoms 787 Heterogen Atoms 248
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling