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LNBase in complex with LNB-LOGNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H04
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 0.2M potassium sodium tartate tetrahydrate, 0.1M sodium citrate, 2.0M ammonium sulfate, pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.79 55.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.759 α = 90 b = 131.617 β = 90 c = 104.606 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 ADSC QUANTUM 270 2014-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
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 50 99.9 0.083 29.4 7.4 175974
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 1.73 100 0.513 3.48 7.3
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 FOURIER SYNTHESIS THROUGHOUT 4H04 1.7 29.94 167078 8805 99.6 0.176 0.175 0.1859 0.206 0.2153 RANDOM 20.31
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.325 r_dihedral_angle_4_deg 19.872 r_dihedral_angle_3_deg 13.787 r_dihedral_angle_1_deg 7.483 r_long_range_B_refined 5.684 r_long_range_B_other 5.642 r_scangle_other 4.507 r_scbond_it 3.057 r_scbond_other 3.053 r_mcangle_it 2.949
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.325 r_dihedral_angle_4_deg 19.872 r_dihedral_angle_3_deg 13.787 r_dihedral_angle_1_deg 7.483 r_long_range_B_refined 5.684 r_long_range_B_other 5.642 r_scangle_other 4.507 r_scbond_it 3.057 r_scbond_other 3.053 r_mcangle_it 2.949 r_mcangle_other 2.949 r_angle_other_deg 2.552 r_angle_refined_deg 2.204 r_mcbond_it 2.143 r_mcbond_other 2.143 r_chiral_restr 0.162 r_bond_refined_d 0.025 r_gen_planes_other 0.018 r_gen_planes_refined 0.013 r_bond_other_d 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 9994 Nucleic Acid Atoms Solvent Atoms 939 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing