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X-ray crystal structure of Rho transcription termination factor in complex with ssRNA substrate and ANPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PV4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 0.05 M Cacodylate (pH 6.5), 0.05 M NaCl, 2.5% PEG 8K, 20% glycerol, 0.3 mM n-Nonyl-beta-D-thiomaltoside, 1mM TCEP,
VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal Properties Matthews coefficient Solvent content 3.14 60.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.249 α = 90 b = 204.649 β = 96.54 c = 147.788 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 95 CCD ADSC QUANTUM 4 mirrors 2003-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.00 ALS 8.3.1
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 3 50 95.7 0.04 0.05 15.3 77507 64912 2.5 2.5 92
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 3 3.12 95 0.274 0.332 2.5 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1PV4 3 20 3 77507 70421 3727 95.7 0.27381 0.27084 0.2391 0.30369 0.245 RANDOM 61.251
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] 0.57 -1.66 1.42 -2.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.096 r_scangle_it 2.579 r_scbond_it 1.43 r_angle_refined_deg 1.252 r_mcangle_it 1.098 r_mcbond_it 0.575 r_nbd_refined 0.248 r_symmetry_vdw_refined 0.225 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.096 r_scangle_it 2.579 r_scbond_it 1.43 r_angle_refined_deg 1.252 r_mcangle_it 1.098 r_mcbond_it 0.575 r_nbd_refined 0.248 r_symmetry_vdw_refined 0.225 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.107 r_symmetry_hbond_refined 0.06 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18846 Nucleic Acid Atoms 200 Solvent Atoms 14 Heterogen Atoms 186
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing