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The set and ring associated (SRA) domain of UHRF1 bound to methylated DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BI7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 12 % PEG 1500, 0.1 M BIS-TRIS, 0.2 M NACL, 0.001 M TCEP, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.25 61.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.198 α = 90 b = 111.359 β = 90.53 c = 97.403 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 300 mm CCD MIRRORS 2008-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.96863 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 40 99.2 0.165 9.77 4.2 81560 81560 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.28 95 0.715 1.35 3.1
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 3BI7 2.2 38.63 81444 77359 4085 99 0.19097 0.1888 0.191 0.23147 0.2309 RANDOM 35.141
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] 0.14 -0.01 -0.14 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.062 r_dihedral_angle_3_deg 16.226 r_dihedral_angle_4_deg 14.234 r_dihedral_angle_1_deg 5.963 r_scangle_it 3.792 r_scbond_it 2.798 r_mcangle_it 2.271 r_angle_refined_deg 1.665 r_mcbond_it 1.457 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.062 r_dihedral_angle_3_deg 16.226 r_dihedral_angle_4_deg 14.234 r_dihedral_angle_1_deg 5.963 r_scangle_it 3.792 r_scbond_it 2.798 r_mcangle_it 2.271 r_angle_refined_deg 1.665 r_mcbond_it 1.457 r_nbtor_refined 0.307 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.163 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.121 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6490 Nucleic Acid Atoms 1948 Solvent Atoms 652 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling