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Crystal Structure of the Periplasmic Nitrate Reductase from Cupriavidus necator
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, SITTING DROP 5.5 293 0.1M bis-Tris pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.63 53.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.202 α = 90 b = 82.384 β = 100.72 c = 96.837 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 4r Sagitally focusing Ge(220) and a multilayer 2006-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 95.346 97.2 0.085 0.085 8.5 3.8 170014 170014
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 95.2 0.537 0.537 1.3 3.8 24265
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 2NAP 1.6 35.48 254265 140809 7066 97.36 0.15875 0.15707 0.1571 0.19031 0.1901 RANDOM 15.87
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] 0.02 0.01 -0.08 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.523 r_dihedral_angle_4_deg 17.011 r_dihedral_angle_3_deg 13.991 r_dihedral_angle_1_deg 6.886 r_scangle_it 4.351 r_scbond_it 2.95 r_angle_refined_deg 2.266 r_mcangle_it 1.778 r_mcbond_it 1.137 r_chiral_restr 0.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.523 r_dihedral_angle_4_deg 17.011 r_dihedral_angle_3_deg 13.991 r_dihedral_angle_1_deg 6.886 r_scangle_it 4.351 r_scbond_it 2.95 r_angle_refined_deg 2.266 r_mcangle_it 1.778 r_mcbond_it 1.137 r_chiral_restr 0.207 r_bond_refined_d 0.028 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7208 Nucleic Acid Atoms Solvent Atoms 672 Heterogen Atoms 190
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection