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Crystal Structure of Adenine Phosphoribosyltransferase (APRT) From Leishmania tarentolae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QB7 PDB ENTRY 1QB7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 277 MOPS 100 mM, 22% isopropanol, Protein at 8 mg/ml, pH 7.00, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.72 54.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.538 α = 90 b = 64.538 β = 90 c = 234.44 γ = 120
Symmetry Space Group P 61 2 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 IMAGE PLATE MARRESEARCH 1999-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 LNLS D03B-MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 28.27 99.5 15513
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 93.1
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 PDB ENTRY 1QB7 2.2 28.27 15513 14724 789 99.5 0.183 0.181 0.1865 0.218 0.2256 RANDOM 24.16
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] 2.01 1.01 2.01 -3.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.99 r_dihedral_angle_3_deg 16.767 r_dihedral_angle_4_deg 11.577 r_dihedral_angle_1_deg 6.619 r_scangle_it 3.251 r_scbond_it 1.952 r_angle_refined_deg 1.494 r_mcangle_it 1.231 r_angle_other_deg 0.871 r_mcbond_it 0.653
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.99 r_dihedral_angle_3_deg 16.767 r_dihedral_angle_4_deg 11.577 r_dihedral_angle_1_deg 6.619 r_scangle_it 3.251 r_scbond_it 1.952 r_angle_refined_deg 1.494 r_mcangle_it 1.231 r_angle_other_deg 0.871 r_mcbond_it 0.653 r_symmetry_vdw_other 0.368 r_symmetry_hbond_refined 0.274 r_nbd_other 0.25 r_xyhbond_nbd_refined 0.233 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.174 r_chiral_restr 0.094 r_nbtor_other 0.086 r_bond_refined_d 0.014 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_xyhbond_nbd_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1650 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 28
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling AMoRE phasing REFMAC refinement HKL-2000 data reduction