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Structure of the PLP synthase complex Pdx1/2 (YaaD/E) from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 15-17% PEG 4000, 200mM tri-ammonium citrate pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.7 54.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.507 α = 90 b = 259.009 β = 92.13 c = 144.962 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 CCD ADSC QUANTUM 210 ESRF 2005-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97626 ESRF ID29
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 2.12 50 98.2 0.081 12 3.1 388915 381798 29
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 2.12 2.14 98.4 0.443 2.1 3.1
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 2NV1 2.12 50 361794 19065 98.18 0.14868 0.14608 0.1568 0.19789 0.2047 RANDOM 34.093
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] 0.94 0.31 -0.43 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.262 r_dihedral_angle_4_deg 19.123 r_dihedral_angle_3_deg 15.956 r_dihedral_angle_1_deg 6.246 r_scangle_it 3.469 r_scbond_it 2.318 r_angle_refined_deg 1.452 r_mcangle_it 1.383 r_mcbond_it 1.043 r_angle_other_deg 0.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.262 r_dihedral_angle_4_deg 19.123 r_dihedral_angle_3_deg 15.956 r_dihedral_angle_1_deg 6.246 r_scangle_it 3.469 r_scbond_it 2.318 r_angle_refined_deg 1.452 r_mcangle_it 1.383 r_mcbond_it 1.043 r_angle_other_deg 0.959 r_symmetry_hbond_refined 0.294 r_symmetry_vdw_other 0.287 r_symmetry_vdw_refined 0.258 r_nbd_refined 0.223 r_nbd_other 0.215 r_xyhbond_nbd_refined 0.194 r_mcbond_other 0.186 r_nbtor_refined 0.175 r_xyhbond_nbd_other 0.101 r_chiral_restr 0.089 r_nbtor_other 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 41883 Nucleic Acid Atoms Solvent Atoms 5774 Heterogen Atoms 203
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing