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Crystal structure of Phl p 4, a grass pollen allergen with glucose dehydrogenase activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other PHL P 4 FROM THE P6122 SPACE GROUP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 293 0.2 M Lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350, 10mM Glucose , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 46.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.774 α = 90 b = 153.437 β = 90 c = 177.631 γ = 90
Symmetry Space Group C 2 2 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 PIXEL PSI PILATUS 6M 2010-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 67.94 99.2 0.061 0.061 9.9 3.7 69488
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 99.4 0.284 0.284 2.5 3.7
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 PHL P 4 FROM THE P6122 SPACE GROUP 2 67.94 65994 65994 3472 100 0.162 0.16 0.1587 0.207 0.2066 RANDOM 22.36
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] 2.2 -0.9 -1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.7 r_dihedral_angle_4_deg 18.172 r_dihedral_angle_3_deg 13.495 r_dihedral_angle_1_deg 6.271 r_scangle_it 3.329 r_scbond_it 2.115 r_angle_refined_deg 1.443 r_mcangle_it 1.294 r_mcbond_it 0.708 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.7 r_dihedral_angle_4_deg 18.172 r_dihedral_angle_3_deg 13.495 r_dihedral_angle_1_deg 6.271 r_scangle_it 3.329 r_scbond_it 2.115 r_angle_refined_deg 1.443 r_mcangle_it 1.294 r_mcbond_it 0.708 r_chiral_restr 0.111 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7684 Nucleic Acid Atoms Solvent Atoms 989 Heterogen Atoms 138
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling