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Crystal structure of the human transglutaminase 1 beta-barrel domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FIE PDB ENTRUES 1EOX, 1FIE, 1GGY, 1G0D AND 1QRK IN AN ENSEMBLE experimental model PDB 1GGY PDB ENTRUES 1EOX, 1FIE, 1GGY, 1G0D AND 1QRK IN AN ENSEMBLE experimental model PDB 1G0D PDB ENTRUES 1EOX, 1FIE, 1GGY, 1G0D AND 1QRK IN AN ENSEMBLE experimental model PDB 1QRK PDB ENTRUES 1EOX, 1FIE, 1GGY, 1G0D AND 1QRK IN AN ENSEMBLE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.7 M (NH4)2SO4, 1% PEG3350, 0.1 M BIS-TRIS (PH 5.5)
Crystal Properties Matthews coefficient Solvent content 2.87 57.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.74 α = 90 b = 115.74 β = 90 c = 115.74 γ = 90
Symmetry Space Group I 4 3 2
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 CCD 2010-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 2.3 19.29 99.6 0.07 21 10.8 6155 2 54.4
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 2.3 2.42 100 0.63 4.1 11.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRUES 1EOX, 1FIE, 1GGY, 1G0D AND 1QRK IN AN ENSEMBLE 2.3 19.29 5852 290 99.59 0.22118 0.21901 0.26688 0.2718 RANDOM 42.281
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.497 r_dihedral_angle_3_deg 17.202 r_dihedral_angle_4_deg 12.862 r_scangle_it 7.705 r_dihedral_angle_1_deg 6.096 r_scbond_it 5.147 r_mcangle_it 3.587 r_mcbond_it 2.002 r_angle_refined_deg 1.829 r_angle_other_deg 0.951
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.497 r_dihedral_angle_3_deg 17.202 r_dihedral_angle_4_deg 12.862 r_scangle_it 7.705 r_dihedral_angle_1_deg 6.096 r_scbond_it 5.147 r_mcangle_it 3.587 r_mcbond_it 2.002 r_angle_refined_deg 1.829 r_angle_other_deg 0.951 r_mcbond_other 0.454 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.004 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_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 705 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing