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Structure of VanYB unbound
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 300 PEG1500, glycerol
Crystal Properties Matthews coefficient Solvent content 1.87 34.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.339 α = 90 b = 40.902 β = 108.44 c = 115.401 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 270 2012-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 0.9791 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.65 30 98.9 38.3 9.9 89220
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 1.65 1.68
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.65 30 43630 2330 98.85 0.17842 0.17679 0.1905 0.20935 0.2198 RANDOM 28.092
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] 0.57 0.86 0.28 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.36 r_dihedral_angle_4_deg 14.902 r_dihedral_angle_3_deg 11.968 r_dihedral_angle_1_deg 5.729 r_long_range_B_refined 5.331 r_long_range_B_other 5.331 r_scangle_other 3.608 r_mcangle_it 2.41 r_mcangle_other 2.409 r_scbond_it 2.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.36 r_dihedral_angle_4_deg 14.902 r_dihedral_angle_3_deg 11.968 r_dihedral_angle_1_deg 5.729 r_long_range_B_refined 5.331 r_long_range_B_other 5.331 r_scangle_other 3.608 r_mcangle_it 2.41 r_mcangle_other 2.409 r_scbond_it 2.349 r_scbond_other 2.348 r_mcbond_it 1.578 r_mcbond_other 1.571 r_angle_refined_deg 1.361 r_angle_other_deg 0.939 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2924 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AutoSol phasing