☰ Navigation Tabs
Crystal structure of fab fragment of anti-Shh 5E1 chimera
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FVE PDB entry 1FVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 292 protein (20 mM Hepes, pH 7.2, 0.1 M NaCl, 5 mM CaCl2) was mixed with equal volumes of reservoir solution (0.2M Ammonium Sulfate, 20% (w/v) PEG 4000), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.01 59.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.287 α = 90 b = 110.287 β = 90 c = 122.509 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 210 2008-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97740 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 100 0.07 15.8 3.2 43883 43883 -3 18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 100 0.482 2.3 3.2 4395
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 PDB entry 1FVE 1.9 44.5 -3 43833 43833 4370 99.99 0.18303 0.18303 0.17853 0.1781 0.22387 0.2224 RANDOM 25.459
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] 0.54 0.27 0.54 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.885 r_dihedral_angle_4_deg 17.397 r_dihedral_angle_3_deg 11.505 r_dihedral_angle_1_deg 6.278 r_scangle_it 4.169 r_mcangle_it 3.32 r_scbond_it 2.834 r_mcbond_it 2.325 r_angle_refined_deg 1.205 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.885 r_dihedral_angle_4_deg 17.397 r_dihedral_angle_3_deg 11.505 r_dihedral_angle_1_deg 6.278 r_scangle_it 4.169 r_mcangle_it 3.32 r_scbond_it 2.834 r_mcbond_it 2.325 r_angle_refined_deg 1.205 r_nbtor_refined 0.298 r_symmetry_hbond_refined 0.204 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3311 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 20
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling