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Crystal structure of monoAc-biotin-avidin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AVD PDB ENTRY 1AVD
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 3.19 61.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.01 α = 90 b = 81.224 β = 92.47 c = 74.41 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 225 mm CCD 2010-04-24
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 1.6 50 98.3 0.087 5.5 176927
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 1.6 1.66 95.4 0.341 5.3
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 THROUGHOUT PDB ENTRY 1AVD 1.6 35.85 176927 8880 97.98 0.1908 0.1895 0.191 0.2148 0.2154 RANDOM 19.6812
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.518 r_dihedral_angle_4_deg 25.112 r_dihedral_angle_3_deg 15.555 r_dihedral_angle_1_deg 6.58 r_scangle_it 6.349 r_scbond_it 4.228 r_mcangle_it 3.05 r_angle_refined_deg 2.925 r_mcbond_it 1.845 r_chiral_restr 0.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.518 r_dihedral_angle_4_deg 25.112 r_dihedral_angle_3_deg 15.555 r_dihedral_angle_1_deg 6.58 r_scangle_it 6.349 r_scbond_it 4.228 r_mcangle_it 3.05 r_angle_refined_deg 2.925 r_mcbond_it 1.845 r_chiral_restr 0.222 r_bond_refined_d 0.035 r_gen_planes_refined 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7648 Nucleic Acid Atoms Solvent Atoms 572 Heterogen Atoms 324
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction HKL-2000 data scaling