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Fab fragment of Der p 1 specific antibody 10B9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 100 mM sodium citrate, 15% w/v PEG 6000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.37 48.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.02 α = 90 b = 121.829 β = 90 c = 55.041 γ = 90
Symmetry Space Group P 21 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 ADSC QUANTUM 210r mirrors 2009-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97918 APS 19-BM
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 1.75 50 99 0.069 0.069 27 5.4 45773 45773 -3
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 1.75 1.78 96.9 0.633 0.633 2.2 4.7
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 3RVT 1.75 50 43428 43428 2318 98.94 0.17065 0.16878 0.1788 0.20587 0.2154 RANDOM 24.238
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] 0.28 -1.04 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.664 r_dihedral_angle_4_deg 20.102 r_dihedral_angle_3_deg 12.442 r_dihedral_angle_1_deg 7.066 r_long_range_B_refined 6.603 r_long_range_B_other 6.353 r_angle_other_deg 3.791 r_scangle_other 3.666 r_scbond_it 2.509 r_scbond_other 2.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.664 r_dihedral_angle_4_deg 20.102 r_dihedral_angle_3_deg 12.442 r_dihedral_angle_1_deg 7.066 r_long_range_B_refined 6.603 r_long_range_B_other 6.353 r_angle_other_deg 3.791 r_scangle_other 3.666 r_scbond_it 2.509 r_scbond_other 2.412 r_mcangle_it 1.903 r_angle_refined_deg 1.882 r_mcangle_other 1.834 r_mcbond_it 1.288 r_mcbond_other 1.288 r_chiral_restr 0.124 r_gen_planes_other 0.02 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3291 Nucleic Acid Atoms Solvent Atoms 445 Heterogen Atoms
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 phasing MOLREP phasing REFMAC refinement Coot model building HKL-3000 data reduction HKL-3000 data scaling