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Crystal structure of AAD-2 in complex with Mn(II) and N-oxalylglycine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GQW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 289 22% PEG 4000
40 mM LiSO4
0.1 M MES pH 6.0
10 mg/mL AAD-2
Cryo: 15% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.52 51.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 266.432 α = 90 b = 55.494 β = 118.97 c = 183.663 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 MARMOSAIC 300 mm CCD 2015-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9787 APS 21-ID-G
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 2.15 50 99 0.088 16.1 4.6 127502
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 92.6 0.72 0.742
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 1GQW 2.15 25 107559 5682 87.89 0.19064 0.18842 0.1892 0.23316 0.2335 RANDOM 35.038
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] -0.39 -0.08 0.76 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.994 r_dihedral_angle_3_deg 13.815 r_dihedral_angle_4_deg 11.727 r_dihedral_angle_1_deg 6.237 r_long_range_B_refined 6.063 r_mcangle_it 2.709 r_scbond_it 1.769 r_mcbond_it 1.569 r_angle_refined_deg 1.29 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.994 r_dihedral_angle_3_deg 13.815 r_dihedral_angle_4_deg 11.727 r_dihedral_angle_1_deg 6.237 r_long_range_B_refined 6.063 r_mcangle_it 2.709 r_scbond_it 1.769 r_mcbond_it 1.569 r_angle_refined_deg 1.29 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 15065 Nucleic Acid Atoms Solvent Atoms 1633 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing