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Crystal structure of the human dok1 PTB domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P5T PDB ENTRY 1P5T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 2M AMONIUM SULFATE, 2% PEG 400, 0.1M NA HEPES PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.39 48.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.88 α = 90 b = 100.168 β = 117.34 c = 67.101 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 2006-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.6 25.98 99.7 0.06 22.5 7.5 59364 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 1.6 1.68 98.3 0.38 2.5 3.6
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 1P5T 1.6 59.66 56366 2997 99.8 0.19 0.188 0.184 0.224 0.2211 RANDOM 21.57
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] 0.3 0.46 -0.61 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.448 r_dihedral_angle_4_deg 17.996 r_dihedral_angle_3_deg 13.698 r_dihedral_angle_1_deg 6.292 r_scangle_it 4.944 r_scbond_it 3.386 r_mcangle_it 2.341 r_mcbond_it 1.614 r_angle_refined_deg 1.557 r_symmetry_vdw_refined 0.454
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.448 r_dihedral_angle_4_deg 17.996 r_dihedral_angle_3_deg 13.698 r_dihedral_angle_1_deg 6.292 r_scangle_it 4.944 r_scbond_it 3.386 r_mcangle_it 2.341 r_mcbond_it 1.614 r_angle_refined_deg 1.557 r_symmetry_vdw_refined 0.454 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.289 r_xyhbond_nbd_refined 0.254 r_nbd_refined 0.206 r_chiral_restr 0.113 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3209 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing