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LNBase in complex with LNB-NHAcDNJ
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 55.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.868 α = 90 b = 131.271 β = 90 c = 104.302 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 1.6 50 90 0.055 18 2.5 189858
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 1.6 1.63 95.2 0.271 2.92 2.3
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 1.6 28.19 180311 9542 90.1 0.183 0.181 0.1913 0.212 0.2203 RANDOM 17.73
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 34.013 r_dihedral_angle_4_deg 18.348 r_dihedral_angle_3_deg 13.695 r_dihedral_angle_1_deg 7.375 r_long_range_B_refined 5.144 r_long_range_B_other 5.117 r_scangle_other 3.809 r_mcangle_it 2.684 r_mcangle_other 2.684 r_scbond_other 2.583
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.013 r_dihedral_angle_4_deg 18.348 r_dihedral_angle_3_deg 13.695 r_dihedral_angle_1_deg 7.375 r_long_range_B_refined 5.144 r_long_range_B_other 5.117 r_scangle_other 3.809 r_mcangle_it 2.684 r_mcangle_other 2.684 r_scbond_other 2.583 r_scbond_it 2.582 r_angle_other_deg 2.549 r_angle_refined_deg 2.262 r_mcbond_it 1.906 r_mcbond_other 1.906 r_chiral_restr 0.161 r_bond_refined_d 0.025 r_gen_planes_other 0.017 r_gen_planes_refined 0.012 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 9974 Nucleic Acid Atoms Solvent Atoms 947 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing