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Human adenylosuccinate lyase in complex with its substrate N6-(1,2- Dicarboxyethyl)-AMP, and its products AMP and fumarate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J91 PDB ENTRY 2J91
Crystallization Crystal Properties Matthews coefficient Solvent content 2.41 48.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.3 α = 90 b = 128.1 β = 90 c = 190.5 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 CCD ADSC CCD 2006-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2 25 99.7 0.06 21.3 7.2 144136
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 2 2.2 99.8 0.38 5.5 7.2
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 2J91 2 50 136929 7207 99.8 0.194 0.192 0.1969 0.229 0.2323 RANDOM 28.83
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] 1.79 0.08 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.108 r_dihedral_angle_4_deg 17.457 r_dihedral_angle_3_deg 13.61 r_dihedral_angle_1_deg 5.263 r_scangle_it 1.717 r_scbond_it 1.165 r_angle_refined_deg 1.088 r_angle_other_deg 0.877 r_mcangle_it 0.648 r_mcbond_it 0.567
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.108 r_dihedral_angle_4_deg 17.457 r_dihedral_angle_3_deg 13.61 r_dihedral_angle_1_deg 5.263 r_scangle_it 1.717 r_scbond_it 1.165 r_angle_refined_deg 1.088 r_angle_other_deg 0.877 r_mcangle_it 0.648 r_mcbond_it 0.567 r_symmetry_vdw_refined 0.3 r_symmetry_vdw_other 0.247 r_nbd_refined 0.199 r_nbd_other 0.181 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.136 r_symmetry_hbond_refined 0.136 r_nbtor_other 0.083 r_chiral_restr 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 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 14706 Nucleic Acid Atoms Solvent Atoms 880 Heterogen Atoms 161
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing