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Crystal structure of the major grass pollen allergen Phl p 2 in complex with its specific IgE-Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U6A PDB ENTRIES 1U6A, 1WH0 experimental model PDB 1WH0 PDB ENTRIES 1U6A, 1WH0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 HANGING DROP DIFFUSION, 1 MICROL PROTEIN (IN 30 MM HEPES, 0.15 M NACL PH 6.8) MIXED WITH 1 MICROL RESERVOIR (20% PEG 3350, 0.2 M NAF)
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.437 α = 90 b = 105.437 β = 90 c = 110.225 γ = 90
Symmetry Space Group P 42 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 MARRESEARCH 2007-07-24 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 1.9 27.56 98.4 0.077 0.07 17.89 5.53 48722
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 1.9 1.92 89.5 0.24 2.43 4.34
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 PDB ENTRIES 1U6A, 1WH0 1.9 30 48678 2466 98.3 0.179 0.177 0.1819 0.226 0.2311 RANDOM 21.76
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] -0.08 -0.08 0.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.473 r_dihedral_angle_4_deg 19.1 r_dihedral_angle_3_deg 11.889 r_scangle_it 8.44 r_scbond_it 7.189 r_dihedral_angle_1_deg 7.088 r_mcangle_it 5.362 r_mcbond_it 4.763 r_angle_refined_deg 1.22 r_angle_other_deg 0.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.473 r_dihedral_angle_4_deg 19.1 r_dihedral_angle_3_deg 11.889 r_scangle_it 8.44 r_scbond_it 7.189 r_dihedral_angle_1_deg 7.088 r_mcangle_it 5.362 r_mcbond_it 4.763 r_angle_refined_deg 1.22 r_angle_other_deg 0.783 r_symmetry_hbond_refined 0.291 r_symmetry_vdw_refined 0.251 r_symmetry_vdw_other 0.225 r_nbd_other 0.2 r_nbd_refined 0.193 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.145 r_nbtor_other 0.085 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_bond_other_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3967 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing