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Phosphotransacetylase from Methanosarcina thermophila soaked 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 5.4 291 ammonium sulfate, sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.95 57.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.469 α = 90 b = 114.469 β = 90 c = 127.832 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 2004-05-06 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 2.6 20 0.066 0.066 26.7 4.5 25264 23999
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) 2.6 2.64 91.4 0.725 0.725 3.2
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 2.6 20 25264 22784 1215 94.99 0.21915 0.21545 0.29017 0.282 RANDOM 72.55
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] 0.91 0.91 -1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.394 r_dihedral_angle_3_deg 19.308 r_dihedral_angle_4_deg 18.98 r_dihedral_angle_1_deg 7.558 r_scangle_it 2.473 r_angle_refined_deg 1.61 r_scbond_it 1.572 r_mcangle_it 0.931 r_mcbond_it 0.53 r_symmetry_hbond_refined 0.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.394 r_dihedral_angle_3_deg 19.308 r_dihedral_angle_4_deg 18.98 r_dihedral_angle_1_deg 7.558 r_scangle_it 2.473 r_angle_refined_deg 1.61 r_scbond_it 1.572 r_mcangle_it 0.931 r_mcbond_it 0.53 r_symmetry_hbond_refined 0.439 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.258 r_nbd_refined 0.243 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4925 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 149
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing