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Crystal structure of the Restriction-Modification Controller Protein C.Csp231I OR 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, HANGING DROP 289 Protein was dialysed against the buffer containing 0.1 M NaCl, 50 mM TRIS-HCl pH 8.0, 1 mM EDTA. Crystallisation conditions: 0.2 M sodium iodide, 0.1 M Bis-Tris Propane pH 6.0, 15 % (w/v) PEG3350, 10 mM spermidine, protein dimer/DNA molar ratio 1:1, protein concentration 4.6 mg/ml
, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.49 50.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.34 α = 90 b = 62.34 β = 90 c = 158.08 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 120 PIXEL PSI PILATUS 6M 2012-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 1.8 53.99 99.5 0.059 12.8 4.2 32091 30476 2
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 1.8 1.9 99.8 0.551 2.6 4
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 1.8 53.99 32091 30476 1614 99.9 0.14788 0.14712 0.1294 0.1626 0.1377 RANDOM 30.616
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] 0.41 0.41 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.751 r_dihedral_angle_4_deg 12.664 r_dihedral_angle_3_deg 11.329 r_dihedral_angle_1_deg 4.041 r_angle_refined_deg 0.952 r_chiral_restr 0.066 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.751 r_dihedral_angle_4_deg 12.664 r_dihedral_angle_3_deg 11.329 r_dihedral_angle_1_deg 4.041 r_angle_refined_deg 0.952 r_chiral_restr 0.066 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 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 1494 Nucleic Acid Atoms 855 Solvent Atoms 402 Heterogen Atoms 4
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALEPACK data scaling