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Avidin related protein AVR4 (C122S, K109I mutant) in complex with BNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y55 PDB Entry 1Y55
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 3. M farmat, 0.1M acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.92 57.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.592 α = 90 b = 77.592 β = 90 c = 109.727 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 4 2005-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.97 ESRF ID14-4
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 1.3 40 99.6 0.036 22 5.4 82848 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 99.6
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB Entry 1Y55 1.3 40 78516 4132 99.84 0.152 0.15183 0.1511 0.1656 RANDOM 12.338
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] -0.11 -0.11 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.072 r_scangle_it 3.007 r_sphericity_free 2.368 r_scbond_it 2.156 r_mcangle_it 1.524 r_sphericity_bonded 1.487 r_angle_refined_deg 1.475 r_rigid_bond_restr 1.209 r_angle_other_deg 0.881 r_mcbond_it 0.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.072 r_scangle_it 3.007 r_sphericity_free 2.368 r_scbond_it 2.156 r_mcangle_it 1.524 r_sphericity_bonded 1.487 r_angle_refined_deg 1.475 r_rigid_bond_restr 1.209 r_angle_other_deg 0.881 r_mcbond_it 0.881 r_chiral_restr 0.428 r_symmetry_vdw_other 0.284 r_nbd_other 0.261 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.102 r_nbtor_other 0.087 r_symmetry_hbond_refined 0.083 r_bond_refined_d 0.011 r_gen_planes_other 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1846 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling