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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 2ZKD PDB ENTRY 2ZKD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M Bis-Tris-propane (pH7.5), 0.2M sodium fluoride, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.62 53.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.878 α = 90 b = 58.878 β = 90 c = 182.309 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 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 2.55 50 99.6 0.079 11160 51.232
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 2.55 2.64 100 0.171 9.2
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 2ZKD 2.55 49.46 10594 532 99.8 0.21716 0.2143 0.2223 0.2745 0.2815 RANDOM 21.456
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] 0.3 0.3 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.009 r_dihedral_angle_4_deg 19.128 r_dihedral_angle_3_deg 18.832 r_dihedral_angle_1_deg 7.127 r_scangle_it 2.482 r_angle_refined_deg 2.012 r_scbond_it 1.584 r_mcangle_it 1.057 r_angle_other_deg 1.017 r_mcbond_it 0.788
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.009 r_dihedral_angle_4_deg 19.128 r_dihedral_angle_3_deg 18.832 r_dihedral_angle_1_deg 7.127 r_scangle_it 2.482 r_angle_refined_deg 2.012 r_scbond_it 1.584 r_mcangle_it 1.057 r_angle_other_deg 1.017 r_mcbond_it 0.788 r_symmetry_vdw_other 0.301 r_symmetry_hbond_refined 0.254 r_nbd_other 0.228 r_nbd_refined 0.211 r_nbtor_refined 0.204 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.163 r_mcbond_other 0.133 r_xyhbond_nbd_other 0.12 r_nbtor_other 0.096 r_chiral_restr 0.089 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 1641 Nucleic Acid Atoms 451 Solvent Atoms 45 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing