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Crystal structure of the RTP:nRB complex from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F4K PDB ENTRY 1F4K (with residues 72 to 88 and the DNA removed)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 295 2% PEG 4000, 125mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.97 58.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.012 α = 90 b = 129.626 β = 90 c = 125.221 γ = 90
Symmetry Space Group C 2 2 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 2003-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.90 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 94.3 0.091 12.7 4.7 32161 1 1 52.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 84.8 0.341 2.3 2.1
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 ENTRY 1F4K (with residues 72 to 88 and the DNA removed) 2.5 50 32161 1729 96.21 0.29303 0.29095 0.2959 0.33221 0.3354 RANDOM 11.106
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] -4.25 -3.33 7.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.025 r_dihedral_angle_3_deg 21.391 r_dihedral_angle_4_deg 19.929 r_dihedral_angle_1_deg 5.665 r_scangle_it 1.694 r_angle_refined_deg 1.532 r_scbond_it 1.041 r_mcangle_it 0.712 r_mcbond_it 0.408 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.025 r_dihedral_angle_3_deg 21.391 r_dihedral_angle_4_deg 19.929 r_dihedral_angle_1_deg 5.665 r_scangle_it 1.694 r_angle_refined_deg 1.532 r_scbond_it 1.041 r_mcangle_it 0.712 r_mcbond_it 0.408 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.247 r_nbd_refined 0.245 r_xyhbond_nbd_refined 0.242 r_symmetry_vdw_refined 0.196 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3787 Nucleic Acid Atoms 1546 Solvent Atoms 24 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing