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Crystal structure of Human Adenylosuccinate Lyase in complex with AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YIS PDB ENTRY 1YIS
Crystallization Crystal Properties Matthews coefficient Solvent content 2.08 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.37 α = 90 b = 104.342 β = 90 c = 213.396 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 2006-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
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 1.8 25 99.8 0.06 19.9 5.8 176155
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 1.8 1.9 100 0.42 4.6 5.8
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 1YIS 1.8 106.6 167346 8809 99.8 0.16 0.157 0.1678 0.199 0.2062 RANDOM 25.81
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] -0.13 -0.46 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.091 r_dihedral_angle_4_deg 19.439 r_dihedral_angle_3_deg 14.455 r_dihedral_angle_1_deg 5.621 r_scangle_it 3.748 r_scbond_it 2.735 r_mcangle_it 1.71 r_angle_refined_deg 1.472 r_mcbond_it 1.463 r_angle_other_deg 0.983
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.091 r_dihedral_angle_4_deg 19.439 r_dihedral_angle_3_deg 14.455 r_dihedral_angle_1_deg 5.621 r_scangle_it 3.748 r_scbond_it 2.735 r_mcangle_it 1.71 r_angle_refined_deg 1.472 r_mcbond_it 1.463 r_angle_other_deg 0.983 r_symmetry_vdw_other 0.267 r_nbd_refined 0.224 r_nbd_other 0.199 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.18 r_symmetry_hbond_refined 0.18 r_symmetry_vdw_refined 0.176 r_chiral_restr 0.086 r_nbtor_other 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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_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 14641 Nucleic Acid Atoms Solvent Atoms 1495 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing