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Crystal structure of the human BTB domain of the Krueppel related Zinc Finger Protein 3 (HKR3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NN2 PDB entry 2NN2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2M MgCl2, 0.1M Bis-tris pH 6.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.38 48.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.375 α = 90 b = 50.375 β = 90 c = 86.093 γ = 120
Symmetry Space Group P 31 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 MARMOSAIC 225 mm CCD 2007-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 0.98248 SRS PX10.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.74 50 100 0.084 0.084 10.6 9.3 13630 13630
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.8 100 0.761 0.761 2.075 7.1 1336
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 PDB entry 2NN2 1.74 43.64 13592 13592 673 99.95 0.188 0.188 0.186 0.2344 0.216 0.2713 RANDOM 28.351
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] 1.02 0.51 1.02 -1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.761 r_dihedral_angle_4_deg 21.97 r_dihedral_angle_3_deg 14.701 r_scangle_it 9.084 r_scbond_it 6.613 r_dihedral_angle_1_deg 5.717 r_mcangle_it 4.729 r_mcbond_it 3.506 r_angle_other_deg 2.295 r_angle_refined_deg 1.548
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.761 r_dihedral_angle_4_deg 21.97 r_dihedral_angle_3_deg 14.701 r_scangle_it 9.084 r_scbond_it 6.613 r_dihedral_angle_1_deg 5.717 r_mcangle_it 4.729 r_mcbond_it 3.506 r_angle_other_deg 2.295 r_angle_refined_deg 1.548 r_mcbond_other 1.058 r_symmetry_vdw_other 0.293 r_nbd_refined 0.232 r_symmetry_vdw_refined 0.193 r_nbd_other 0.192 r_nbtor_refined 0.192 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.149 r_nbtor_other 0.1 r_chiral_restr 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 852 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection