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Structure of the synthase subunit Pdx1.1 (Snz1) of PLP synthase from Saccharomyces cerevisiae
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, SITTING DROP 8 291 4M formate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 4.81 74.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.073 α = 90 b = 154.218 β = 90 c = 154.868 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 ADSC QUANTUM 4 TOROIDAL (ESRF) 2007-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 3.02 20 99.8 0.075 23.4 7.9 72026 72026 -4 79.3
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 3.02 3.05 96.2 0.416 3.4 6.5
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 (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 3.02 20 71521 69465 2053 99.66 0.16267 0.16215 0.2234 0.18097 0.2217 RANDOM 32.98
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] -8.08 -9.07 17.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.96 r_dihedral_angle_3_deg 23.629 r_dihedral_angle_4_deg 22.197 r_dihedral_angle_1_deg 6.408 r_scangle_it 3.581 r_mcangle_it 2.644 r_scbond_it 2.269 r_mcbond_it 1.372 r_angle_refined_deg 1.284 r_angle_other_deg 0.894
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.96 r_dihedral_angle_3_deg 23.629 r_dihedral_angle_4_deg 22.197 r_dihedral_angle_1_deg 6.408 r_scangle_it 3.581 r_mcangle_it 2.644 r_scbond_it 2.269 r_mcbond_it 1.372 r_angle_refined_deg 1.284 r_angle_other_deg 0.894 r_symmetry_vdw_other 0.377 r_symmetry_vdw_refined 0.294 r_nbd_refined 0.278 r_mcbond_other 0.25 r_nbd_other 0.225 r_nbtor_refined 0.194 r_xyhbond_nbd_refined 0.186 r_nbtor_other 0.098 r_chiral_restr 0.063 r_xyhbond_nbd_other 0.054 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_refined 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 12594 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling