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Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZKG PDB ENTRY 2ZKG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.1M sodium citrate (pH5.6), 0.2M sodium acetate, 30% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.45 49.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.587 α = 90 b = 104.036 β = 99.18 c = 65.586 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 100 CCD ADSC QUANTUM 315 undulator 2008-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.6 50 99.1 0.062 77879 20.136
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 1.6 1.66 91.9 0.329 3.2 7102
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 2ZKG 1.6 28.24 73317 3872 99.12 0.15636 0.15483 0.1637 0.18452 0.1927 RANDOM 17.825
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] -0.43 -0.11 0.94 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.512 r_dihedral_angle_4_deg 17.096 r_dihedral_angle_3_deg 11.49 r_dihedral_angle_1_deg 5.582 r_scangle_it 1.985 r_angle_refined_deg 1.515 r_scbond_it 1.444 r_angle_other_deg 0.968 r_mcangle_it 0.889 r_mcbond_it 0.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.512 r_dihedral_angle_4_deg 17.096 r_dihedral_angle_3_deg 11.49 r_dihedral_angle_1_deg 5.582 r_scangle_it 1.985 r_angle_refined_deg 1.515 r_scbond_it 1.444 r_angle_other_deg 0.968 r_mcangle_it 0.889 r_mcbond_it 0.776 r_nbd_other 0.226 r_nbd_refined 0.2 r_symmetry_vdw_other 0.194 r_nbtor_refined 0.19 r_symmetry_hbond_refined 0.184 r_mcbond_other 0.151 r_xyhbond_nbd_refined 0.14 r_symmetry_vdw_refined 0.136 r_nbtor_other 0.084 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3283 Nucleic Acid Atoms 974 Solvent Atoms 663 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing