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Deoxyribose-phosphate aldolase from P. yoelii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JCL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 298 PEG4K, Tris pH 8.5, NaCl 0.2 M, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.17 42.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.121 α = 90 b = 143.472 β = 106.24 c = 50.156 γ = 90
Symmetry Space Group P 1 21 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 CCD SBC-3 2005-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
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 1.85 34.68 98 0.68 20.3 3.5 41400 -3
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 1.85 1.92 87.2 0.501 1.56 2.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1JCL 1.84 34.68 41400 39307 2092 97.34 0.20503 0.2028 0.2483 0.2414 RANDOM 33.875
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] -0.25 -0.23 -1.12 1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.56 r_dihedral_angle_3_deg 13.948 r_dihedral_angle_4_deg 12.231 r_dihedral_angle_1_deg 5.935 r_scangle_it 3.951 r_scbond_it 2.748 r_mcangle_it 2.115 r_mcbond_it 1.378 r_angle_refined_deg 1.147 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.56 r_dihedral_angle_3_deg 13.948 r_dihedral_angle_4_deg 12.231 r_dihedral_angle_1_deg 5.935 r_scangle_it 3.951 r_scbond_it 2.748 r_mcangle_it 2.115 r_mcbond_it 1.378 r_angle_refined_deg 1.147 r_nbtor_refined 0.299 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.08 r_symmetry_hbond_refined 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined 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 3906 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing