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Crystal Structure of Yeast Pyridoxal 5-Phosphate Synthase Snz1 Complxed with Substrate PLP
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 7.5 289 20% PEG 400, 0.1M Megnesium Cloride, 0.1M HEPES, 2.5mM PLP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.66 53.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.972 α = 90 b = 109.421 β = 90 c = 155.389 γ = 90
Symmetry Space Group P 2 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 273 CCD RAYONIX MX-225 2009-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.0 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 32.4 99.2 51330 51330 2 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 97.4
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 MIR THROUGHOUT 1znn 2.2 32.4 51330 48770 2625 98.87 0.19563 0.19399 0.1935 0.2274 0.2237 RANDOM 44.336
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] 1.19 -0.51 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.36 r_dihedral_angle_4_deg 23.463 r_dihedral_angle_3_deg 15.862 r_scangle_it 13.295 r_scbond_it 8.964 r_mcangle_it 6.345 r_dihedral_angle_1_deg 5.275 r_mcbond_it 4.672 r_angle_refined_deg 1.095 r_nbtor_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.36 r_dihedral_angle_4_deg 23.463 r_dihedral_angle_3_deg 15.862 r_scangle_it 13.295 r_scbond_it 8.964 r_mcangle_it 6.345 r_dihedral_angle_1_deg 5.275 r_mcbond_it 4.672 r_angle_refined_deg 1.095 r_nbtor_refined 0.325 r_symmetry_hbond_refined 0.301 r_symmetry_vdw_refined 0.298 r_nbd_refined 0.246 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5871 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 48
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling