☰ Navigation Tabs
Human SAHH-like domain of human adenosylhomocysteinase 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D64 PDB ENTRY 3D64
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 0.1M HEPES, 12.5% PEG3350, 0.2M sodium malonate, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.21 61.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.188 α = 90 b = 164.188 β = 90 c = 184.614 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 Q315r mirrors 2009-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.98 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.25 19.91 99.9 0.104 0.104 33.2 29.6 119253 0.102
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.25 2.37 100 0.507 0.516 9 29.8 17219
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 PDB ENTRY 3D64 2.25 19.91 117967 1204 100 0.18231 0.18186 0.1874 0.22581 0.2276 RANDOM 32.781
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] 0.02 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.618 r_dihedral_angle_4_deg 17.46 r_dihedral_angle_3_deg 15.411 r_dihedral_angle_1_deg 6.612 r_scangle_it 3.293 r_scbond_it 2.209 r_angle_refined_deg 1.513 r_mcangle_it 1.369 r_mcbond_it 0.94 r_angle_other_deg 0.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.618 r_dihedral_angle_4_deg 17.46 r_dihedral_angle_3_deg 15.411 r_dihedral_angle_1_deg 6.612 r_scangle_it 3.293 r_scbond_it 2.209 r_angle_refined_deg 1.513 r_mcangle_it 1.369 r_mcbond_it 0.94 r_angle_other_deg 0.924 r_symmetry_vdw_other 0.248 r_nbd_refined 0.219 r_nbd_other 0.196 r_mcbond_other 0.189 r_symmetry_vdw_refined 0.187 r_symmetry_hbond_refined 0.187 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.174 r_nbtor_other 0.089 r_chiral_restr 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13415 Nucleic Acid Atoms Solvent Atoms 582 Heterogen Atoms 176
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling