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X-ray structure of biotin binding protein from chicken
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WBI PDB ENTRY 1WBI
Crystallization Crystal Properties Matthews coefficient Solvent content 2.06 39.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.652 α = 90 b = 56.049 β = 90 c = 57.126 γ = 90
Symmetry Space Group P 21 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 100 CCD MARRESEARCH 2005-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
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 1.75 25 99.9 0.01 13 4.8 26447 -3
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 1.75 1.85 100 0.05 3 4.8
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 1WBI 1.75 25 25104 1342 99.9 0.195 0.193 0.1919 0.233 0.2312 RANDOM 22.8
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] 0.1 1.25 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.907 r_dihedral_angle_4_deg 13.632 r_dihedral_angle_3_deg 13.397 r_dihedral_angle_1_deg 5.928 r_scangle_it 3.559 r_scbond_it 2.356 r_mcangle_it 1.676 r_angle_refined_deg 1.595 r_mcbond_it 1.011 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.907 r_dihedral_angle_4_deg 13.632 r_dihedral_angle_3_deg 13.397 r_dihedral_angle_1_deg 5.928 r_scangle_it 3.559 r_scbond_it 2.356 r_mcangle_it 1.676 r_angle_refined_deg 1.595 r_mcbond_it 1.011 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.21 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.113 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1928 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing