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Phosphotransacetylase from Methanosarcina thermophila co-crystallized with coenzyme A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QZT PDB ENTRY 1QZT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 sodium citrate, HEPES, Coenzyme A, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.08 59.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.488 α = 90 b = 116.488 β = 90 c = 127.46 γ = 90
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 4 doubly focusing toroidal mirror 2004-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.1 NSLS X26C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.147 20 0.066 0.066 24 4.2 46290 45391
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.147 2.19 99.2 0.427 0.427 2.38 4.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1QZT 2.147 20 46290 43035 2356 98.06 0.20646 0.20297 0.27228 0.2113 RANDOM 60.125
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] -1.24 -1.24 2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.064 r_dihedral_angle_3_deg 18.499 r_dihedral_angle_4_deg 13.848 r_dihedral_angle_1_deg 7.158 r_scangle_it 3.126 r_scbond_it 2.012 r_angle_refined_deg 1.761 r_mcangle_it 1.091 r_angle_other_deg 0.9 r_mcbond_it 0.837
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.064 r_dihedral_angle_3_deg 18.499 r_dihedral_angle_4_deg 13.848 r_dihedral_angle_1_deg 7.158 r_scangle_it 3.126 r_scbond_it 2.012 r_angle_refined_deg 1.761 r_mcangle_it 1.091 r_angle_other_deg 0.9 r_mcbond_it 0.837 r_nbd_refined 0.241 r_xyhbond_nbd_refined 0.237 r_symmetry_vdw_other 0.214 r_nbd_other 0.193 r_mcbond_other 0.185 r_nbtor_refined 0.182 r_symmetry_vdw_refined 0.164 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_other 0.105 r_chiral_restr 0.096 r_nbtor_other 0.089 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4918 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing