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Crystal structure of ZHX1 HD4 (zinc-fingers and homeoboxes protein 1, homeodomain 4)
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, HANGING DROP 5.6 294 2.5M ammonium sulphate, 10mM magnesium acetate, MES pH5.6, 20mM ATP, 20mM phenol, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 1.71118 28.119759
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.9 α = 90 b = 48.8 β = 104.02 c = 49.32 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 IMAGE PLATE MAR scanner 345 mm plate 2005-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.541
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 2.6 30 99.7 0.102 24.3 8.3 4674 -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) 2.6 2.69 99.1 0.339 5.5 6.5 453
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 2.6 19.45 4459 214 99.6 0.20149 0.19926 0.1999 0.25039 0.2532 RANDOM 28.994
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] 0.61 0.42 0.35 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.151 r_dihedral_angle_3_deg 14.266 r_dihedral_angle_4_deg 9.586 r_dihedral_angle_1_deg 3.533 r_angle_refined_deg 1.021 r_angle_other_deg 0.734 r_chiral_restr 0.276 r_bond_refined_d 0.007 r_bond_other_d 0.004 r_gen_planes_refined 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.151 r_dihedral_angle_3_deg 14.266 r_dihedral_angle_4_deg 9.586 r_dihedral_angle_1_deg 3.533 r_angle_refined_deg 1.021 r_angle_other_deg 0.734 r_chiral_restr 0.276 r_bond_refined_d 0.007 r_bond_other_d 0.004 r_gen_planes_refined 0.003 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1172 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 5
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling