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Human chromodomain Y-like protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FBM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 300 12% Isopropanol, 0.2M NaCitrate, 0.1M
NaCacodylate pH 5.0., VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.83 56.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.207 α = 90 b = 132.739 β = 102.92 c = 100.361 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 2006-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 39.37 96 73681 73681
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.97 70
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 2fbm 1.9 39.37 69775 69775 3674 95.97 0.19139 0.19139 0.18912 0.1884 0.23332 0.2325 RANDOM 34.706
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] 0.02 0.06 -0.04 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.943 r_dihedral_angle_4_deg 18.857 r_dihedral_angle_3_deg 16.533 r_dihedral_angle_1_deg 6.314 r_scangle_it 4.866 r_scbond_it 3.149 r_mcangle_it 1.909 r_angle_refined_deg 1.668 r_mcbond_it 1.209 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.943 r_dihedral_angle_4_deg 18.857 r_dihedral_angle_3_deg 16.533 r_dihedral_angle_1_deg 6.314 r_scangle_it 4.866 r_scbond_it 3.149 r_mcangle_it 1.909 r_angle_refined_deg 1.668 r_mcbond_it 1.209 r_nbtor_refined 0.301 r_symmetry_hbond_refined 0.287 r_symmetry_vdw_refined 0.261 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.114 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5965 Nucleic Acid Atoms Solvent Atoms 532 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction DENZO data reduction SCALEPACK data scaling MOLREP phasing