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Crystal Structure of TrkA glyceraldehyde-3-phosphate dehydrogenase from Brucella melitensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OBF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 289 JCSG+ screen well B2, 20% PEG 3350, 0.2 M sodium isothiocyanate, , pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.975 α = 90 b = 106.333 β = 107.89 c = 90.776 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
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 2.4 50 97.8 0.15 11.6 3.5 49106
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) 2.4 2.49 98.4 0.444 2.4 3.5 4907
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 1OBF 2.4 50 49077 2471 96.91 0.187 0.185 0.1892 0.225 0.1951 RANDOM 22.613
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] 0.44 0.02 0.24 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.003 r_dihedral_angle_4_deg 19.712 r_dihedral_angle_3_deg 19.308 r_dihedral_angle_1_deg 6.232 r_scangle_it 2.561 r_scbond_it 1.578 r_angle_refined_deg 1.467 r_mcangle_it 0.998 r_mcbond_it 0.524 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.003 r_dihedral_angle_4_deg 19.712 r_dihedral_angle_3_deg 19.308 r_dihedral_angle_1_deg 6.232 r_scangle_it 2.561 r_scbond_it 1.578 r_angle_refined_deg 1.467 r_mcangle_it 0.998 r_mcbond_it 0.524 r_chiral_restr 0.098 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10164 Nucleic Acid Atoms Solvent Atoms 521 Heterogen Atoms 176
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction