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Crystal structure of the GluA2o LBD in complex with ZK200775 and Compound-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FTJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.9 277 15% PEG 3350, 0.1 M SODIUM ACETATE, 0.1 M ZINC ACETATE
Crystal Properties Matthews coefficient Solvent content 2.16 43.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.384 α = 90 b = 56.565 β = 91.74 c = 90.779 γ = 90
Symmetry Space Group P 1 21 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 315r 2013-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.976486 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.25 50 93.1 0.053 19.5 3.3 128359
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 59 0.517 1.8 2.4
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 1FTJ 1.25 40 121789 6437 93.02 0.17053 0.16946 0.171 0.19034 0.1918 RANDOM 16.829
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 0.26 -0.34 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.445 r_dihedral_angle_4_deg 15.642 r_dihedral_angle_3_deg 11.417 r_dihedral_angle_1_deg 5.753 r_long_range_B_refined 4.574 r_scbond_it 2.033 r_mcangle_it 1.54 r_angle_refined_deg 1.499 r_mcbond_it 1.009 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.445 r_dihedral_angle_4_deg 15.642 r_dihedral_angle_3_deg 11.417 r_dihedral_angle_1_deg 5.753 r_long_range_B_refined 4.574 r_scbond_it 2.033 r_mcangle_it 1.54 r_angle_refined_deg 1.499 r_mcbond_it 1.009 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 4058 Nucleic Acid Atoms Solvent Atoms 652 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing