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Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N5W PDB code 1N5W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 291 0.2 M Magnesium sulfate heptahydrate, 20% w/v Polyethylene glycol 3,350, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.36 47.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.627 α = 90 b = 114.818 β = 90 c = 154.316 γ = 90
Symmetry Space Group P 21 21 21
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 mirrors 2008-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9793 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 2.402 34.81 95.6 0.108 7.3 6.7 75718 75718 42.08
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 2.402 2.44 88.7 0.6 2.1 5.5 3435
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 code 1N5W 2.402 34.81 71176 71176 3763 94.58 0.195 0.195 0.191 0.1931 0.266 0.2668 RANDOM 23.632
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] -1.69 2.58 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.567 r_dihedral_angle_4_deg 18.946 r_dihedral_angle_3_deg 18.486 r_dihedral_angle_1_deg 6.475 r_scangle_it 4.188 r_scbond_it 2.586 r_angle_refined_deg 1.792 r_mcangle_it 1.467 r_mcbond_it 0.79 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.567 r_dihedral_angle_4_deg 18.946 r_dihedral_angle_3_deg 18.486 r_dihedral_angle_1_deg 6.475 r_scangle_it 4.188 r_scbond_it 2.586 r_angle_refined_deg 1.792 r_mcangle_it 1.467 r_mcbond_it 0.79 r_chiral_restr 0.114 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 14621 Nucleic Acid Atoms Solvent Atoms 667 Heterogen Atoms 143
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 data collection BALBES phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling