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Crystal structure of the Restriction-Modification Controller Protein C.Csp231I OL operator complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LFP PDB entry 3LFP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 Protein was dialysed against the buffer containing 0.1 M NaCl, 50 mM TRIS-HCl pH 8.2, 1 mM DTT, and 1 mM EDTA. Crystallisation conditions: 0.2 M sodium nitrate, 0.1 M Bis-Tris-Propane pH 7.5, 24 % (w/v) PEG3350, protein dimer/DNA molar ratio 1:1, protein concentration 1.46 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.85 56.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.12 α = 90 b = 128.07 β = 99.99 c = 78.54 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 120 CCD ADSC QUANTUM 315r 2010-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.93930 ESRF ID14-4
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 2.75 36 97.6 0.075 9 3.9 20836 20336 2 43.3
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 2.75 2.94 89 0.304 2.9 3.1 3378
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 (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 3LFP 2.75 35.06 20833 19280 1041 97.49 0.20672 0.20511 0.2048 0.23532 0.2341 RANDOM 50.112
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] -0.05 0.19 0.19 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.699 r_dihedral_angle_3_deg 13.69 r_dihedral_angle_4_deg 10.936 r_dihedral_angle_1_deg 3.433 r_angle_refined_deg 0.863 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.699 r_dihedral_angle_3_deg 13.69 r_dihedral_angle_4_deg 10.936 r_dihedral_angle_1_deg 3.433 r_angle_refined_deg 0.863 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3076 Nucleic Acid Atoms 1710 Solvent Atoms 51 Heterogen Atoms
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling