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Structure of Hub-1 protein in complex with Snu66 peptide (HINDI)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBI PDB entry 1UBI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 290 20% PEG 3350, 0.2M Ammonium Chloride, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 1.84 33.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.23 α = 83.44 b = 36.34 β = 89.85 c = 36.78 γ = 85.84
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD MAR CCD 165 mm mirrors 2006-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6
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 1.4 30 94.6 35599 33677 2 2
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) 1 1.4 1.5 92.4 0.318 5.56
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 1UBI 1.4 26.12 2 33677 31992 1686 94.63 0.18737 0.18521 0.1945 0.22819 0.2347 RANDOM 18.696
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] -0.12 0.11 -0.05 0.17 -0.01 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.795 r_dihedral_angle_3_deg 10.527 r_dihedral_angle_4_deg 7.488 r_dihedral_angle_1_deg 5.229 r_sphericity_bonded 3.273 r_sphericity_free 2.956 r_scangle_it 2.934 r_scbond_it 1.885 r_mcangle_it 1.704 r_rigid_bond_restr 1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.795 r_dihedral_angle_3_deg 10.527 r_dihedral_angle_4_deg 7.488 r_dihedral_angle_1_deg 5.229 r_sphericity_bonded 3.273 r_sphericity_free 2.956 r_scangle_it 2.934 r_scbond_it 1.885 r_mcangle_it 1.704 r_rigid_bond_restr 1.13 r_mcbond_it 1.125 r_angle_refined_deg 1.033 r_nbtor_refined 0.298 r_symmetry_vdw_refined 0.185 r_nbd_refined 0.177 r_symmetry_hbond_refined 0.1 r_xyhbond_nbd_refined 0.096 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1443 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling