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Plasmodium vivax adenylosuccinate lyase Pv003765 with AMP bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HVG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 2M Ammonia Sulfate, 0.2M K/Na Tartrate, 0.1M Na Citrate pH5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.37 63.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.247 α = 90 b = 179.545 β = 99.37 c = 68.575 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 IMAGE PLATE RIGAKU RAXIS IV++ 2007-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.01 50 99.9 0.102 13.48 3.7 93338 93338
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.08 99.9 0.54 2.3 3.5 9285
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2hvg 2.01 33.83 88647 88647 4686 99.82 0.17693 0.1752 0.1742 0.21013 0.2083 RANDOM 28.845
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] 0.04 -0.08 -1.11 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.723 r_dihedral_angle_3_deg 13.468 r_dihedral_angle_4_deg 13.081 r_dihedral_angle_1_deg 6.293 r_scangle_it 3.626 r_scbond_it 2.428 r_angle_refined_deg 1.531 r_mcangle_it 1.499 r_mcbond_it 0.959 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.723 r_dihedral_angle_3_deg 13.468 r_dihedral_angle_4_deg 13.081 r_dihedral_angle_1_deg 6.293 r_scangle_it 3.626 r_scbond_it 2.428 r_angle_refined_deg 1.531 r_mcangle_it 1.499 r_mcbond_it 0.959 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.228 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.188 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.107 r_symmetry_metal_ion_refined 0.05 r_metal_ion_refined 0.047 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7297 Nucleic Acid Atoms Solvent Atoms 833 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling MOLREP phasing