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Crystal structure of IdnL7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AMU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 299 0.1M Tris, 0.2M magnesium chloride, 30% PEG4000, 0.5mM [N-(L-alanyl)sulfamoyl] adenosine
Crystal Properties Matthews coefficient Solvent content 2.3 46.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.526 α = 90 b = 68.526 β = 90 c = 225.169 γ = 90
Symmetry Space Group P 41 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 2015-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00 Photon Factory AR-NW12A
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 2.1 50 99.7 0.101 33.4 13.9 32390
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 2.1 2.14 100 0.954 2.6 14.2
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 1AMU 2.1 43.54 30667 1642 99.69 0.17946 0.17732 0.1838 0.22031 0.2183 RANDOM 43.169
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] 0.3 0.3 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.974 r_dihedral_angle_4_deg 18.577 r_dihedral_angle_3_deg 14.939 r_dihedral_angle_1_deg 6.248 r_angle_refined_deg 1.844 r_angle_other_deg 0.885 r_chiral_restr 0.109 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.974 r_dihedral_angle_4_deg 18.577 r_dihedral_angle_3_deg 14.939 r_dihedral_angle_1_deg 6.248 r_angle_refined_deg 1.844 r_angle_other_deg 0.885 r_chiral_restr 0.109 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 3682 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing