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Crystal Structure of E. coli Tryptophanase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AX4 PDB ENTRY 1AX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.9 1.6M AMMONIUM SULFATE, 0.5%(V/V)PEG400, 0.1M SODIUM HEPES PH 7.9
Crystal Properties Matthews coefficient Solvent content 2.96 58.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 215.51 α = 90 b = 215.51 β = 90 c = 107.56 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 110 CCD ADSC CCD RH-COATED FUSED SILICA COLLIMATING MIRROR 2002-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C NSLS X8C
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 2.8 500 99.3 0.09 26.9 6.6 62257
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 2.8 2.91 98.8 0.24 8.7
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 1AX4 2.8 500 62257 3150 99.3 0.164 0.196 0.1921 0.22 0.2128 RANDOM 8.8
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] -1.529 -1.529 3.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.895 r_dihedral_angle_3_deg 22.423 r_dihedral_angle_4_deg 21.001 r_dihedral_angle_1_deg 9.361 r_scangle_it 4.614 r_scbond_it 2.91 r_angle_refined_deg 2.683 r_mcangle_it 1.613 r_mcbond_it 0.847 r_nbtor_refined 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.895 r_dihedral_angle_3_deg 22.423 r_dihedral_angle_4_deg 21.001 r_dihedral_angle_1_deg 9.361 r_scangle_it 4.614 r_scbond_it 2.91 r_angle_refined_deg 2.683 r_mcangle_it 1.613 r_mcbond_it 0.847 r_nbtor_refined 0.34 r_nbd_refined 0.289 r_symmetry_vdw_refined 0.236 r_symmetry_hbond_refined 0.228 r_chiral_restr 0.187 r_xyhbond_nbd_refined 0.178 r_bond_refined_d 0.031 r_gen_planes_refined 0.01 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14282 Nucleic Acid Atoms Solvent Atoms 518 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing