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Crystal structure of L3MBTL1 MBT Domain with MBK14970
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RJD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 30% PEG 400, 0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES pH7.5
Crystal Properties Matthews coefficient Solvent content 3.1 60.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.88 α = 90 b = 93.166 β = 90 c = 58.444 γ = 90
Symmetry Space Group P 21 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 RIGAKU SATURN A200 2016-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.74 50 99.8 0.075 0.082 0.031 10.7 6.7 48892
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.77 97.3 0.748 0.841 0.376 0.65 4.7
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 2RJD 1.74 27 46176 2434 99.45 0.2014 0.2003 0.2119 0.2216 0.23 RANDOM 26.273
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] -0.46 0.98 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.18 r_dihedral_angle_4_deg 22.742 r_dihedral_angle_3_deg 11.332 r_dihedral_angle_1_deg 6.1 r_angle_refined_deg 1.425 r_angle_other_deg 0.914 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.18 r_dihedral_angle_4_deg 22.742 r_dihedral_angle_3_deg 11.332 r_dihedral_angle_1_deg 6.1 r_angle_refined_deg 1.425 r_angle_other_deg 0.914 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2491 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction HKL-3000 data reduction