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Crystal structure of Xenavidin
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 2.71 54.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.853 α = 90 b = 110.853 β = 90 c = 143.778 γ = 120
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 ADSC CCD 2006-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.7 25 100 0.07 21.99 9.1 37484 -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 1.7 1.8 100 0.51 4.19 9.2
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 (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 1.7 79.81 35613 1871 99.9 0.166 0.165 0.1626 0.19 0.1871 RANDOM 28.05
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] 0.26 0.13 0.26 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.457 r_dihedral_angle_4_deg 20.42 r_dihedral_angle_3_deg 13.866 r_dihedral_angle_1_deg 6.777 r_scangle_it 3.257 r_scbond_it 2.156 r_angle_refined_deg 1.538 r_mcangle_it 1.441 r_mcbond_it 0.969 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.457 r_dihedral_angle_4_deg 20.42 r_dihedral_angle_3_deg 13.866 r_dihedral_angle_1_deg 6.777 r_scangle_it 3.257 r_scbond_it 2.156 r_angle_refined_deg 1.538 r_mcangle_it 1.441 r_mcbond_it 0.969 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.216 r_symmetry_hbond_refined 0.208 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 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 1911 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing