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Crystal structure of Ara h 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S7E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 15% PEG400, 150 mM NaCl, 100 mM Na citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.02 39.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.886 α = 90 b = 92.886 β = 90 c = 231.552 γ = 120
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 315r mirrors 2011-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
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 2.35 50 100 0.088 0.088 30.6 5.6 31048 31048 -3 49.3
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 2.35 2.39 100 0.628 0.628 3.4 5.6 1563
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 3S7E 2.35 40.13 25512 25512 1386 86.53 0.20489 0.20489 0.20273 0.2188 0.24373 0.2393 RANDOM 54.129
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] 8.09 8.09 -16.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.547 r_dihedral_angle_4_deg 21.028 r_dihedral_angle_3_deg 17.631 r_dihedral_angle_1_deg 7.059 r_scangle_it 3.209 r_scbond_it 2.196 r_angle_refined_deg 1.682 r_angle_other_deg 1.144 r_mcangle_it 1.084 r_mcbond_it 0.604
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.547 r_dihedral_angle_4_deg 21.028 r_dihedral_angle_3_deg 17.631 r_dihedral_angle_1_deg 7.059 r_scangle_it 3.209 r_scbond_it 2.196 r_angle_refined_deg 1.682 r_angle_other_deg 1.144 r_mcangle_it 1.084 r_mcbond_it 0.604 r_mcbond_other 0.217 r_chiral_restr 0.099 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5587 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 2
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 phasing MOLREP phasing REFMAC refinement Coot model building CCP4 refinement HKL-2000 data reduction HKL-2000 data scaling