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Structure of the synthase subunit Pdx1 (YaaD) of PLP synthase from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZNN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 15-20% ethanol, 200mM MgCl2, 100mM Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.47 50.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.055 α = 90 b = 106.202 β = 90 c = 182.332 γ = 90
Symmetry Space Group P 21 21 2
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 4 ESRF 2005-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97625 ESRF ID23-1
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 2.08 50 98.6 0.103 9 3.3 118303 116594 25
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 2.08 2.1 99.5 0.479 2.1 3.3
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 1ZNN 2.08 48.68 110798 5782 98.59 0.14414 0.14163 0.1514 0.19139 0.2007 RANDOM 28.452
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] 0.25 -0.07 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.496 r_dihedral_angle_3_deg 12.798 r_dihedral_angle_4_deg 9.751 r_dihedral_angle_1_deg 6.043 r_scangle_it 3.972 r_scbond_it 2.616 r_mcangle_it 1.603 r_angle_refined_deg 1.506 r_mcbond_it 1.03 r_angle_other_deg 0.976
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.496 r_dihedral_angle_3_deg 12.798 r_dihedral_angle_4_deg 9.751 r_dihedral_angle_1_deg 6.043 r_scangle_it 3.972 r_scbond_it 2.616 r_mcangle_it 1.603 r_angle_refined_deg 1.506 r_mcbond_it 1.03 r_angle_other_deg 0.976 r_symmetry_vdw_other 0.296 r_nbd_refined 0.232 r_symmetry_hbond_refined 0.232 r_mcbond_other 0.214 r_nbd_other 0.212 r_xyhbond_nbd_refined 0.21 r_symmetry_vdw_refined 0.182 r_nbtor_refined 0.173 r_chiral_restr 0.09 r_nbtor_other 0.088 r_xyhbond_nbd_other 0.086 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.003 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 11340 Nucleic Acid Atoms Solvent Atoms 2367 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing