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Crystal structure of Bs-CspB in complex with rU6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CSP PDB ENTRY 1CSP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293.15 protein buffer: 50mM TRIS, 20mM Na-HEPES, pH 7.5; Bs-CspB.rU6 complex concentration: 70mg/ml; crystallization buffer: 31% PEG 3350, 0.25M MgCl2, 0.1M TRIS pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 1.91 35.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.038 α = 90 b = 49.769 β = 90 c = 57.38 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 110 IMAGE PLATE MAR scanner 345 mm plate mirrors, slits 2009-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.68 17.5 96.08 0.079 10.48 2.87 15961 15961 -3 25.148
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 1.68 1.72 93.7 0.545 1.85 2.84 1033
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1CSP 1.68 17.46 15162 15162 798 100 0.18252 0.18252 0.1798 0.23466 0.2372 RANDOM 16.765
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] -0.44 1.65 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.33 r_dihedral_angle_4_deg 24.603 r_dihedral_angle_3_deg 10.619 r_dihedral_angle_1_deg 5.846 r_scangle_it 3.465 r_scbond_it 2.603 r_angle_refined_deg 1.459 r_mcangle_it 1.341 r_mcbond_it 1.093 r_angle_other_deg 0.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.33 r_dihedral_angle_4_deg 24.603 r_dihedral_angle_3_deg 10.619 r_dihedral_angle_1_deg 5.846 r_scangle_it 3.465 r_scbond_it 2.603 r_angle_refined_deg 1.459 r_mcangle_it 1.341 r_mcbond_it 1.093 r_angle_other_deg 0.981 r_mcbond_other 0.283 r_symmetry_vdw_other 0.237 r_nbd_refined 0.187 r_nbtor_refined 0.183 r_nbd_other 0.173 r_symmetry_vdw_refined 0.149 r_xyhbond_nbd_refined 0.108 r_symmetry_hbond_refined 0.094 r_nbtor_other 0.086 r_chiral_restr 0.068 r_bond_refined_d 0.016 r_metal_ion_refined 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1036 Nucleic Acid Atoms 117 Solvent Atoms 178 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling