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Crystal structure of the N-terminal domain of NusG (NGN) from Methanocaldococcus jannaschii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EXU PDB CODE 2EXU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 29% (v/v) dioxane, 20mM Bis-Tris propane pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.89 34.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.951 α = 90 b = 39.951 β = 90 c = 83.147 γ = 120
Symmetry Space Group P 32 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 IMAGE PLATE MAR scanner 345 mm plate 2008-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.038 34.606 97.6 78.6 8.8 5232
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 2.03 2.1 84.1 17.1 6
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 PDB CODE 2EXU 2.04 26.59 4710 507 99.03 0.19933 0.19682 0.1973 0.22454 0.2244 RANDOM 35.301
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] 1.27 0.64 1.27 -1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.106 r_dihedral_angle_3_deg 14.555 r_dihedral_angle_4_deg 13.123 r_dihedral_angle_1_deg 4.911 r_scangle_it 1.737 r_scbond_it 1.016 r_angle_refined_deg 1.015 r_mcangle_it 0.733 r_mcbond_it 0.655 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.106 r_dihedral_angle_3_deg 14.555 r_dihedral_angle_4_deg 13.123 r_dihedral_angle_1_deg 4.911 r_scangle_it 1.737 r_scbond_it 1.016 r_angle_refined_deg 1.015 r_mcangle_it 0.733 r_mcbond_it 0.655 r_nbtor_refined 0.296 r_symmetry_vdw_refined 0.184 r_nbd_refined 0.183 r_xyhbond_nbd_refined 0.12 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 610 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 12
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling