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Application of anti-helix antibodies in protein structure determination (8188cys-3LRHcys)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6K64
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 296 45% PEG 4000,
0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.78 30.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.227 α = 87.16 b = 40.603 β = 75.2 c = 61.691 γ = 65.5
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 103 CCD ADSC QUANTUM 315 2016-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.979 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 50 94.8 0.035 27.2 2.8 21978
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 0.091
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 FREE R-VALUE 6K64 1.94 25.99 19954 2023 94.32 0.17366 0.16938 0.1781 0.21525 0.2216 RANDOM 28.649
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] 0.33 0.03 -0.05 -0.19 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.746 r_dihedral_angle_4_deg 17.249 r_dihedral_angle_3_deg 12.999 r_long_range_B_refined 7.629 r_long_range_B_other 7.52 r_dihedral_angle_1_deg 5.869 r_scangle_other 5.713 r_mcangle_it 3.855 r_mcangle_other 3.855 r_scbond_it 3.673
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.746 r_dihedral_angle_4_deg 17.249 r_dihedral_angle_3_deg 12.999 r_long_range_B_refined 7.629 r_long_range_B_other 7.52 r_dihedral_angle_1_deg 5.869 r_scangle_other 5.713 r_mcangle_it 3.855 r_mcangle_other 3.855 r_scbond_it 3.673 r_scbond_other 3.671 r_mcbond_it 2.731 r_mcbond_other 2.729 r_angle_refined_deg 1.558 r_angle_other_deg 1.442 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2495 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing