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Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Bartonella henselae with bound NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DOC PDB entry 3DOC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 Hampton Research CSHT condition H4, 0.1 M Tris pH 8.5, 25% v/v tert-butanol,
23.7 mg/mL protein, crystal tracking ID 206078h4, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.55 51.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.776 α = 90 b = 91.776 β = 90 c = 161.402 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315r 2009-12-03 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 2.5 50 94.8 0.082 16.1 4.1 26594
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 2.5 2.59 96.2 0.59 2.39 4.1 2657
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 3DOC 2.5 38.59 26592 1343 94.91 0.204 0.202 0.1995 0.249 0.2496 RANDOM 29.076
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] 1.15 0.58 1.15 -1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.397 r_dihedral_angle_4_deg 21.66 r_dihedral_angle_3_deg 15.685 r_dihedral_angle_1_deg 6.293 r_scangle_it 2.478 r_scbond_it 1.567 r_angle_refined_deg 1.454 r_mcangle_it 1.007 r_mcbond_it 0.535 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.397 r_dihedral_angle_4_deg 21.66 r_dihedral_angle_3_deg 15.685 r_dihedral_angle_1_deg 6.293 r_scangle_it 2.478 r_scbond_it 1.567 r_angle_refined_deg 1.454 r_mcangle_it 1.007 r_mcbond_it 0.535 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4941 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 88
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling