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Crystal Structure of the Lipocalin domain of Violaxanthin de-epoxidase (VDE) at pH7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CQR AtVDE at pH5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 298 PEG3350, MgNO3, Benzamidine HCl, pH 7, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.36 43.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.634 α = 82.52 b = 52.458 β = 75.99 c = 54.605 γ = 74.54
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 315 2006-03-19 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 Merge I (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 30 96.9 0.088 0.088 6.2 2 23574 23574 1 1 20.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 97.1 0.344 0.344 1.6 2 6787
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 AtVDE at pH5 2 30 22270 22270 1199 96.87 0.2 0.2 0.196 0.206 0.272 0.276 RANDOM 34.02
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] -0.23 -0.02 -0.11 0.09 0.02 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.227 r_dihedral_angle_4_deg 22.792 r_dihedral_angle_3_deg 19.421 r_dihedral_angle_1_deg 9.226 r_scangle_it 4.838 r_scbond_it 3.344 r_angle_refined_deg 2.205 r_mcangle_it 2.189 r_mcbond_it 1.389 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.227 r_dihedral_angle_4_deg 22.792 r_dihedral_angle_3_deg 19.421 r_dihedral_angle_1_deg 9.226 r_scangle_it 4.838 r_scbond_it 3.344 r_angle_refined_deg 2.205 r_mcangle_it 2.189 r_mcbond_it 1.389 r_nbtor_refined 0.326 r_nbd_refined 0.257 r_symmetry_vdw_refined 0.257 r_symmetry_hbond_refined 0.215 r_xyhbond_nbd_refined 0.212 r_chiral_restr 0.191 r_bond_refined_d 0.022 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2603 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection