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CpG specific methyltransferase in complex with target DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C7P PDB entry 2C7P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 294 10% PEG 3350, 150 mM NaCl, 50 mM sodium. For cryoprotection glycerol was added to 25% v/v, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.74 55.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.95 α = 90 b = 83.95 β = 90 c = 173.84 γ = 90
Symmetry Space Group P 41 21 2
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 ADSC QUANTUM 315 BENT MIRRORS 2010-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.15 40 99.3 0.078 0.078 5.5 3.9 34324 34324 33.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.27 99.9 0.31 0.31 2.5 4 4957
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2C7P 2.15 38.6 34274 34274 1729 98.96 0.17832 0.17832 0.17632 0.1771 0.21631 0.2178 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.254 r_dihedral_angle_4_deg 15.209 r_dihedral_angle_3_deg 15.063 r_dihedral_angle_1_deg 6.16 r_angle_other_deg 3.966 r_angle_refined_deg 1.253 r_symmetry_vdw_other 0.38 r_nbd_other 0.232 r_nbd_refined 0.192 r_nbtor_refined 0.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.254 r_dihedral_angle_4_deg 15.209 r_dihedral_angle_3_deg 15.063 r_dihedral_angle_1_deg 6.16 r_angle_other_deg 3.966 r_angle_refined_deg 1.253 r_symmetry_vdw_other 0.38 r_nbd_other 0.232 r_nbd_refined 0.192 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.137 r_nbtor_other 0.108 r_symmetry_hbond_refined 0.084 r_symmetry_vdw_refined 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d r_chiral_restr r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 3199 Nucleic Acid Atoms 570 Solvent Atoms 267 Heterogen Atoms 32
Software Software Software Name Purpose ADSC data collection MOLREP phasing CHAINSAW model building REFMAC refinement ARP/wARP model building MOSFLM data reduction SCALA data scaling CHAINSAW phasing REFMAC phasing