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Crystal Structure of purine nucleoside phosphorylase DeoD from Bacillus anthracis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ECP PDB ENTRY 1ECP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 PEG 400, magnesium chloride, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal Properties Matthews coefficient Solvent content 3 58.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.861 α = 90 b = 128.257 β = 90 c = 223.565 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 120 IMAGE PLATE MARRESEARCH osmic multilayer mirrors 2004-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54189
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 2.24 20 90.9 0.141 3.9 81257 81257
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) 2.24 2.32 82 0.502 1.84 3.2 7218
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 (All) 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 1ECP 2.24 20 81055 81055 4065 100 0.18369 0.18369 0.18097 0.1879 0.23523 0.2408 RANDOM 20.373
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] 0.56 0.18 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.894 r_dihedral_angle_3_deg 18.661 r_dihedral_angle_4_deg 14.394 r_dihedral_angle_1_deg 6.807 r_scangle_it 2.567 r_scbond_it 1.685 r_angle_refined_deg 1.538 r_angle_other_deg 0.963 r_mcangle_it 0.907 r_mcbond_it 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.894 r_dihedral_angle_3_deg 18.661 r_dihedral_angle_4_deg 14.394 r_dihedral_angle_1_deg 6.807 r_scangle_it 2.567 r_scbond_it 1.685 r_angle_refined_deg 1.538 r_angle_other_deg 0.963 r_mcangle_it 0.907 r_mcbond_it 0.75 r_symmetry_vdw_other 0.317 r_symmetry_vdw_refined 0.217 r_nbd_refined 0.192 r_nbd_other 0.191 r_nbtor_refined 0.174 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.166 r_mcbond_other 0.113 r_chiral_restr 0.108 r_nbtor_other 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10728 Nucleic Acid Atoms Solvent Atoms 716 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing