☰ Navigation Tabs
Crystal structure of methyladenine demethylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IE3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 286 5% PEG3350, 5% MPD, 100mM CaCl2, 200mM NaF, 100mM Bis-Tris pH6.5
Crystal Properties Matthews coefficient Solvent content 3.05 59.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.017 α = 106.6 b = 99.17 β = 90.42 c = 126.793 γ = 93.14
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2017-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97929 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.8 50.01 93 0.065 0.056 0.978 11.2 3.7 72797
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.85 0.72 0.556 0.643
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 6IE3 2.8 50.01 69068 3700 71.2 0.21835 0.21644 0.2229 0.25357 0.226 RANDOM 52.212
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] 0.48 0.06 -0.88 1.53 -0.5 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.745 r_dihedral_angle_3_deg 16.811 r_dihedral_angle_4_deg 16.518 r_long_range_B_refined 6.823 r_long_range_B_other 6.816 r_dihedral_angle_1_deg 6.596 r_mcangle_it 3.889 r_mcangle_other 3.889 r_scangle_other 3.172 r_mcbond_it 2.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.745 r_dihedral_angle_3_deg 16.811 r_dihedral_angle_4_deg 16.518 r_long_range_B_refined 6.823 r_long_range_B_other 6.816 r_dihedral_angle_1_deg 6.596 r_mcangle_it 3.889 r_mcangle_other 3.889 r_scangle_other 3.172 r_mcbond_it 2.217 r_mcbond_other 2.216 r_scbond_it 1.75 r_scbond_other 1.75 r_angle_refined_deg 1.241 r_angle_other_deg 0.919 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20086 Nucleic Acid Atoms Solvent Atoms 486 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing