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Transglutaminase 2 undergoes large conformational change upon activation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KV3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.25 298 100 mM HEPES pH 7.25, 1.25M Amm. sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.54 51.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.671 α = 90 b = 71.671 β = 90 c = 309.01 γ = 90
Symmetry Space Group P 41 21 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 QUANTUM 315 2006-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9794 SSRL BL11-1
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 94.9 0.072 11.8 6.3 53209 53209
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 2.09 78.2 0.296 2.38 4.5 5332
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 1KV3 2 25 53209 53209 3482 100 0.231 0.228 0.2284 0.266 0.2675 RANDOM 39.305
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] 1.3 1.3 -2.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.904 r_dihedral_angle_3_deg 17.398 r_dihedral_angle_4_deg 15.947 r_dihedral_angle_1_deg 7.01 r_scangle_it 2.34 r_scbond_it 1.614 r_angle_refined_deg 1.361 r_mcangle_it 1.049 r_mcbond_it 0.865 r_angle_other_deg 0.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.904 r_dihedral_angle_3_deg 17.398 r_dihedral_angle_4_deg 15.947 r_dihedral_angle_1_deg 7.01 r_scangle_it 2.34 r_scbond_it 1.614 r_angle_refined_deg 1.361 r_mcangle_it 1.049 r_mcbond_it 0.865 r_angle_other_deg 0.862 r_nbd_other 0.202 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.178 r_symmetry_hbond_refined 0.164 r_mcbond_other 0.156 r_symmetry_vdw_other 0.137 r_symmetry_vdw_refined 0.1 r_nbtor_other 0.088 r_chiral_restr 0.085 r_xyhbond_nbd_other 0.019 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5232 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 25
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection PHASER phasing