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Anthranilate phosphoribosyl-transferase (TRPD) double mutant D83G F149S from S. solfataricus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZYK PDB ENTRY 1ZYK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 18% PEG (w/v) 1500, 10% glycerol (v/v), 50mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.945 α = 90 b = 65.993 β = 98.81 c = 84.262 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 PIXEL PSI PILATUS 6M 2008-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.725 SLS X06SA
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 2.25 46.08 98.7 0.048 21.3 3.37 31695
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 2.25 2.3 97.6 0.382 5.1 3.44 1996
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 1ZYK 2.25 20 30691 1003 100 0.19383 0.19169 0.195 0.25954 0.2596 RANDOM 24.986
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] 0.51 0.94 -1.59 1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.853 r_dihedral_angle_3_deg 16.016 r_dihedral_angle_4_deg 15.233 r_scangle_it 8.542 r_scbond_it 6.755 r_dihedral_angle_1_deg 5.595 r_mcangle_it 4.187 r_mcbond_it 3.786 r_angle_other_deg 1.596 r_angle_refined_deg 1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.853 r_dihedral_angle_3_deg 16.016 r_dihedral_angle_4_deg 15.233 r_scangle_it 8.542 r_scbond_it 6.755 r_dihedral_angle_1_deg 5.595 r_mcangle_it 4.187 r_mcbond_it 3.786 r_angle_other_deg 1.596 r_angle_refined_deg 1.16 r_mcbond_other 0.919 r_metal_ion_refined 0.34 r_symmetry_vdw_other 0.242 r_nbd_refined 0.187 r_chiral_restr 0.181 r_nbd_other 0.179 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.124 r_symmetry_vdw_refined 0.121 r_symmetry_hbond_refined 0.12 r_nbtor_other 0.088 r_bond_refined_d 0.007 r_bond_other_d 0.007 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5237 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 74
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling XDS data scaling