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Crystal structure of small subunit (R.BspD6I2) of the heterodimeric restriction endonuclease R.BspD6I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EWF PDB ENTRY 2ewf
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10.5 298 2.0 M (NH4)2SO4, 0.2 M Li2SO4, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 1.99 38.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.429 α = 90 b = 38.36 β = 101.47 c = 61.995 γ = 90
Symmetry Space Group P 1 21 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 CCD MAR CCD 165 mm AU-COATED PLANAR and TOROIDAL MIRRORS 2006-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6
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 1.5 20 99.3 0.054 21.2 2.91 29298 28430 2 18.66
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 1.5 1.53 0.47 2.24 2.87 1428
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 2ewf 1.5 10.75 28355 1428 99.37 0.179 0.177 0.1765 0.211 0.2097 RANDOM 18.891
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] 0.33 -0.36 -0.89 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.515 r_dihedral_angle_4_deg 15.856 r_dihedral_angle_3_deg 14.078 r_dihedral_angle_1_deg 4.694 r_scangle_it 4.003 r_scbond_it 2.579 r_mcangle_it 1.541 r_angle_refined_deg 1.421 r_mcbond_it 0.986 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.515 r_dihedral_angle_4_deg 15.856 r_dihedral_angle_3_deg 14.078 r_dihedral_angle_1_deg 4.694 r_scangle_it 4.003 r_scbond_it 2.579 r_mcangle_it 1.541 r_angle_refined_deg 1.421 r_mcbond_it 0.986 r_nbtor_refined 0.315 r_symmetry_hbond_refined 0.262 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1533 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Best data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing