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Crystal Structure of the Pob3 middle domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Wild-type protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 21% PEG 3350, 20% Glycerol, 200mM NaCl, 50mM Ammonium Sulphate, 100mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.17 43.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.868 α = 90 b = 157.527 β = 89.77 c = 57.787 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 4 2005-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.0000 NSLS X26C
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 2.49 78 91.1 34206 31162
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.49 2.59 92.8
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 (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 Wild-type protein 2.55 78.81 34206 29326 1542 91.66 0.21926 0.21472 0.2166 0.30287 0.2986 RANDOM 10.237
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] 2.41 1 -0.44 -1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.947 r_dihedral_angle_4_deg 20.663 r_dihedral_angle_3_deg 20.123 r_dihedral_angle_1_deg 8.105 r_scangle_it 2.068 r_angle_refined_deg 1.504 r_scbond_it 1.347 r_mcangle_it 0.791 r_mcbond_it 0.442 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.947 r_dihedral_angle_4_deg 20.663 r_dihedral_angle_3_deg 20.123 r_dihedral_angle_1_deg 8.105 r_scangle_it 2.068 r_angle_refined_deg 1.504 r_scbond_it 1.347 r_mcangle_it 0.791 r_mcbond_it 0.442 r_nbtor_refined 0.32 r_nbd_refined 0.234 r_symmetry_hbond_refined 0.219 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7569 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling PHASER phasing