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Crystal structure of NPC-biotin-avidin complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 2.5-2.7M ammonium sulfate, 0.1M sodium citrate(pH 4.0-5.0), vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.09 60.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.02 α = 90 b = 73.535 β = 120.02 c = 81.18 γ = 90
Symmetry Space Group C 1 2 1
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 RAYONIX MX225HE 2010-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 50 98.2 0.068 10.1 4.3 44266
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 2 2.03 97.1 0.424 4.4 2211
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 37.52 44247 2228 98.19 0.1907 0.1885 0.1895 0.2303 0.2299 RANDOM 28.2242
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.923 r_dihedral_angle_4_deg 22.657 r_dihedral_angle_3_deg 18.039 r_dihedral_angle_1_deg 7.722 r_scangle_it 5.876 r_scbond_it 3.835 r_angle_refined_deg 2.709 r_mcangle_it 2.658 r_mcbond_it 1.537 r_chiral_restr 0.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.923 r_dihedral_angle_4_deg 22.657 r_dihedral_angle_3_deg 18.039 r_dihedral_angle_1_deg 7.722 r_scangle_it 5.876 r_scbond_it 3.835 r_angle_refined_deg 2.709 r_mcangle_it 2.658 r_mcbond_it 1.537 r_chiral_restr 0.194 r_bond_refined_d 0.029 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3821 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 218
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling