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Crystal structure of the periplasmic nitrate reductase (NAP) from Escherichia coli
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, HANGING DROP 5.6 294 20% PEG 4000, 10% 2-propanol, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.41 49.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.449 α = 90 b = 94.596 β = 96.34 c = 131.211 γ = 90
Symmetry Space Group P 1 21 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 2003-09-15 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) 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 2.5 50 97.3 0.108 0.108 5.4 2.5 56862 56852
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) 2.5 2.64 97.8 0.365 0.365 1.4 2.3
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 2.5 50 56833 53973 2860 97.11 0.18435 0.18113 0.1811 0.24314 0.2412 RANDOM 28.451
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] 3.12 3.15 -3.08 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.375 r_dihedral_angle_3_deg 19.397 r_dihedral_angle_4_deg 18.245 r_dihedral_angle_1_deg 7.468 r_scangle_it 2.612 r_scbond_it 1.675 r_angle_refined_deg 1.631 r_mcangle_it 1.058 r_mcbond_it 0.638 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.375 r_dihedral_angle_3_deg 19.397 r_dihedral_angle_4_deg 18.245 r_dihedral_angle_1_deg 7.468 r_scangle_it 2.612 r_scbond_it 1.675 r_angle_refined_deg 1.631 r_mcangle_it 1.058 r_mcbond_it 0.638 r_nbtor_refined 0.318 r_symmetry_hbond_refined 0.273 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.192 r_symmetry_vdw_refined 0.181 r_chiral_restr 0.111 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 12604 Nucleic Acid Atoms Solvent Atoms 925 Heterogen Atoms 206
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction CCP4 data scaling MOLREP phasing