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Signal Recognition Particle Receptor Beta-Subunit in nucleotide-free dimerized form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NRJ PDB ENTRY 1NRJ chain B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH UNDER PARAFFIN OIL 5.5 277 1.3M ammonium sulfate, 50mM Bis/Tris/HCl, 0.5mM GDP, 5mM magnesium chloride, 5mM Hepes, 125mM sodium chloride, 2.5mM DTT, 0.25mM EDTA, pH 5.5, MICROBATCH UNDER PARAFFIN OIL, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.99 58.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.996 α = 90 b = 74.996 β = 90 c = 158.475 γ = 120
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 MAR CCD 165 mm 2003-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9A 1.00944 NSLS X9A
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 33.8 98.6 0.074 24.2 5.6 33853 33373 1 49.4
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 (All) 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 1NRJ chain B 2.2 25 2 25288 22942 2527 99.75 0.223 0.18832 0.18264 0.1915 0.23941 0.2386 RANDOM 38.144
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] 1.76 0.88 1.76 -2.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.851 r_dihedral_angle_4_deg 23.28 r_dihedral_angle_3_deg 18.004 r_dihedral_angle_1_deg 6.729 r_scangle_it 4.815 r_scbond_it 3.301 r_mcangle_it 2.331 r_angle_refined_deg 1.894 r_mcbond_it 1.641 r_angle_other_deg 1.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.851 r_dihedral_angle_4_deg 23.28 r_dihedral_angle_3_deg 18.004 r_dihedral_angle_1_deg 6.729 r_scangle_it 4.815 r_scbond_it 3.301 r_mcangle_it 2.331 r_angle_refined_deg 1.894 r_mcbond_it 1.641 r_angle_other_deg 1.086 r_mcbond_other 0.299 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.214 r_nbd_other 0.198 r_nbtor_refined 0.181 r_symmetry_vdw_other 0.18 r_symmetry_vdw_refined 0.147 r_chiral_restr 0.125 r_symmetry_hbond_refined 0.12 r_nbtor_other 0.092 r_bond_refined_d 0.024 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2591 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling BEAST phasing