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Crystal structure of ZHX2 HD2 (zinc-fingers and homeoboxes protein 2, homeodomain 2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ECC PDB ENTRY 2ecc
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 20% PEG 6000, 0.2M LiCl, HEPES pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.54 51.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.71 α = 90 b = 60.67 β = 95.34 c = 27.71 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 MARMOSAIC 225 mm CCD 2005-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.976 ESRF BM14
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 2.7 30 100 0.111 15.4 5.6 4459 -1.5
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) 2.7 2.8 100 0.451 3.1 5.6 449
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 2ecc 2.7 28.38 4214 240 99.91 0.20664 0.20329 0.2038 0.26684 0.2648 RANDOM 35.638
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] 4.2 0.15 -3.53 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.475 r_dihedral_angle_3_deg 16.407 r_dihedral_angle_4_deg 14.874 r_scangle_it 6.397 r_dihedral_angle_1_deg 4.841 r_scbond_it 4.7 r_mcangle_it 3.647 r_mcbond_it 2.888 r_angle_refined_deg 0.902 r_angle_other_deg 0.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.475 r_dihedral_angle_3_deg 16.407 r_dihedral_angle_4_deg 14.874 r_scangle_it 6.397 r_dihedral_angle_1_deg 4.841 r_scbond_it 4.7 r_mcangle_it 3.647 r_mcbond_it 2.888 r_angle_refined_deg 0.902 r_angle_other_deg 0.784 r_mcbond_other 0.674 r_symmetry_vdw_other 0.249 r_nbd_refined 0.198 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.166 r_nbd_other 0.156 r_symmetry_vdw_refined 0.138 r_symmetry_hbond_refined 0.125 r_nbtor_other 0.084 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other 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 938 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 5
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling