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avidin related protein (AVR4)-BNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y52 PDB Entry 1y52
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 3.0M format, 0.1 M acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.06 59.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.039 α = 90 b = 78.039 β = 90 c = 110.028 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 2004-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 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 1.05 40 99.2 0.054 34.7 5.4 157254 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 1.05 1.07 99.2
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 MOLECULAR REPLACEMENT THROUGHOUT PDB Entry 1y52 1.05 40 149834 7908 99.96 0.1675 0.16711 0.16659 0.17708 RANDOM 11.764
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] -0.13 -0.13 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.861 r_scangle_it 2.963 r_sphericity_free 2.219 r_sphericity_bonded 2.207 r_scbond_it 1.899 r_mcangle_it 1.491 r_angle_refined_deg 1.414 r_rigid_bond_restr 1.009 r_mcbond_it 0.871 r_angle_other_deg 0.853
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.861 r_scangle_it 2.963 r_sphericity_free 2.219 r_sphericity_bonded 2.207 r_scbond_it 1.899 r_mcangle_it 1.491 r_angle_refined_deg 1.414 r_rigid_bond_restr 1.009 r_mcbond_it 0.871 r_angle_other_deg 0.853 r_chiral_restr 0.431 r_nbd_other 0.26 r_symmetry_vdw_other 0.241 r_nbd_refined 0.238 r_symmetry_hbond_refined 0.123 r_symmetry_vdw_refined 0.117 r_xyhbond_nbd_refined 0.088 r_nbtor_other 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1894 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing