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Alanine aminotransferase from Pyrococcus furiosus Pfu-1397077-001
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GD9 PDB ENTRY 1GD9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 291 15%w/v PEG-3350, 0.4 micromoles per liter cesium chloride, 0.15M ammonium citrate, pH 7.4, modified microbatch, temperature 291K, pH 7.40
Crystal Properties Matthews coefficient Solvent content 2.28 45.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.804 α = 90 b = 188.089 β = 89.79 c = 72.583 γ = 90
Symmetry Space Group P 1 21 1
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 SBC-3 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
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 2.33 50 98.6 0.053 69038
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 2.33 2.42 91.2 0.23
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1GD9 2.33 42.26 68993 2100 100 0.20335 0.202 0.2017 0.245 0.2419 THIN SHELLS 27.17
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] -0.072 -0.055 0.046 0.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.766 r_dihedral_angle_4_deg 17.82 r_dihedral_angle_3_deg 14.23 r_dihedral_angle_1_deg 5.541 r_scangle_it 3.55 r_mcangle_it 2.998 r_scbond_it 2.416 r_mcbond_it 1.829 r_angle_refined_deg 1.471 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.766 r_dihedral_angle_4_deg 17.82 r_dihedral_angle_3_deg 14.23 r_dihedral_angle_1_deg 5.541 r_scangle_it 3.55 r_mcangle_it 2.998 r_scbond_it 2.416 r_mcbond_it 1.829 r_angle_refined_deg 1.471 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.216 r_nbd_refined 0.192 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.1 r_symmetry_hbond_refined 0.075 r_bond_refined_d 0.013 r_gen_planes_refined 0.003 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12162 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 60
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing