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P domain of GII.17-2014/15
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PUN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 11% (w/v) polyethylene glycol (PEG) 3350, 4%(v/v) Tacsimate (pH7.0)
Crystal Properties Matthews coefficient Solvent content 2.26 45.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.612 α = 90 b = 87.151 β = 90 c = 95.998 γ = 90
Symmetry Space Group P 21 21 21
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 315r 2016-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 1.0 SSRF BL17U1
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 50 97.8 0.121 23.6 5.4 42553
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 2 2.03 87.2 0.397 3 3
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 3PUN 2 50 40343 2153 96.37 0.19597 0.19393 0.201 0.23389 0.2379 RANDOM 30.594
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] 0.72 -2.65 1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.933 r_dihedral_angle_4_deg 16.197 r_dihedral_angle_3_deg 11.486 r_dihedral_angle_1_deg 6.579 r_long_range_B_refined 5.292 r_long_range_B_other 5.066 r_scangle_other 2.959 r_mcangle_it 2.656 r_mcangle_other 2.656 r_scbond_it 1.803
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.933 r_dihedral_angle_4_deg 16.197 r_dihedral_angle_3_deg 11.486 r_dihedral_angle_1_deg 6.579 r_long_range_B_refined 5.292 r_long_range_B_other 5.066 r_scangle_other 2.959 r_mcangle_it 2.656 r_mcangle_other 2.656 r_scbond_it 1.803 r_scbond_other 1.803 r_mcbond_it 1.661 r_mcbond_other 1.659 r_angle_refined_deg 1.244 r_angle_other_deg 0.829 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4813 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing