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Crystal structure of Escherichia coli NrfA with Europium bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RDZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 Crystals were obtained in 100 mM HEPES pH 7.5, 20 % PEG 10 K. Soaked in mother liqour containing 10 mM Eu(II)Cl, 20 % Ethylene glycol for 2 minutes before immersion in liquid nitrogen., VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.57 52.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.884 α = 90 b = 90.489 β = 90 c = 292.196 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 ADSC QUANTUM 4 2001-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 0.9795 SRS PX14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 146.1 98.5 0.079 11.6 3.01 139682 16.4
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 2.053 93.28 0.313 8.73 2.72 9181
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2RDZ 2 146.1 132196 6985 98.16 0.16646 0.16355 0.1657 0.22194 0.2252 RANDOM 20.12
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] 2.28 -0.55 -1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.503 r_dihedral_angle_4_deg 16.494 r_dihedral_angle_3_deg 15.058 r_dihedral_angle_1_deg 6.413 r_scangle_it 4.759 r_scbond_it 3.237 r_angle_refined_deg 1.854 r_mcangle_it 1.825 r_mcbond_it 1.082 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.503 r_dihedral_angle_4_deg 16.494 r_dihedral_angle_3_deg 15.058 r_dihedral_angle_1_deg 6.413 r_scangle_it 4.759 r_scbond_it 3.237 r_angle_refined_deg 1.854 r_mcangle_it 1.825 r_mcbond_it 1.082 r_chiral_restr 0.127 r_bond_refined_d 0.023 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13904 Nucleic Acid Atoms Solvent Atoms 2050 Heterogen Atoms 873
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling