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Transglutaminase2 complexed with calcium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PYG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 Potassium chloride, Magnesium acetate tetrahydrate, Sodium cacodylate, Polyethylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 2.58 52.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.08 α = 90 b = 216.307 β = 90 c = 166.263 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 125 CCD ADSC QUANTUM 315r 2011-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.00000 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.55 42.585 99.99 0.113 8.95 10.9 29265
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.56 3.62 0.391
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4PYG 3.55 42.585 29242 1490 99.595 0.228 0.2266 0.2166 0.2619 0.2548 60.856
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] 0.016 -0.003 -0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.499 r_dihedral_angle_4_deg 19.17 r_dihedral_angle_3_deg 18.582 r_lrange_it 8.545 r_lrange_other 8.545 r_scangle_it 7.949 r_scangle_other 7.939 r_mcangle_it 6.724 r_mcangle_other 6.724 r_scbond_it 5.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.499 r_dihedral_angle_4_deg 19.17 r_dihedral_angle_3_deg 18.582 r_lrange_it 8.545 r_lrange_other 8.545 r_scangle_it 7.949 r_scangle_other 7.939 r_mcangle_it 6.724 r_mcangle_other 6.724 r_scbond_it 5.799 r_scbond_other 5.79 r_dihedral_angle_1_deg 4.603 r_mcbond_it 4.431 r_mcbond_other 4.431 r_angle_other_deg 2.311 r_angle_refined_deg 1.676 r_nbd_other 0.336 r_symmetry_xyhbond_nbd_refined 0.308 r_symmetry_nbd_other 0.26 r_symmetry_nbd_refined 0.251 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.208 r_xyhbond_nbd_other 0.193 r_nbtor_refined 0.189 r_symmetry_xyhbond_nbd_other 0.125 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.085 r_bond_other_d 0.036 r_gen_planes_other 0.029 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15665 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling PHASER phasing Coot model building