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Phosphopentomutase 4H11 variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M8Z PDB ENTRY 3M8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.45 293 20 mg/mL protein in 1 mM manganese chloride, 25 mM Tris-HCl, pH 7.4 against a reservoir of 25% PEG3350, 50 mM ammonium sulfate, 100 mM Bis-Tris, pH 5.45, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.293 α = 90 b = 60.492 β = 98.5 c = 78.854 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 MARMOSAIC 300 mm CCD 2013-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.979 APS 21-ID-G
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 1.78 50 99.5 0.073 15.3 34906 -3
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 1.78 1.81 99.7 0.253 3.3
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 3M8Z 1.78 39.02 33487 33246 1644 99.28 0.14169 0.13976 0.1542 0.17964 0.1911 RANDOM 14.063
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] 0.09 0.27 0.08 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.867 r_dihedral_angle_4_deg 14.753 r_dihedral_angle_3_deg 13.137 r_dihedral_angle_1_deg 6.301 r_long_range_B_refined 5.97 r_long_range_B_other 5.969 r_scangle_other 3.747 r_scbond_it 2.445 r_scbond_other 2.445 r_angle_refined_deg 2.028
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.867 r_dihedral_angle_4_deg 14.753 r_dihedral_angle_3_deg 13.137 r_dihedral_angle_1_deg 6.301 r_long_range_B_refined 5.97 r_long_range_B_other 5.969 r_scangle_other 3.747 r_scbond_it 2.445 r_scbond_other 2.445 r_angle_refined_deg 2.028 r_mcangle_it 1.731 r_mcangle_other 1.73 r_mcbond_it 1.142 r_mcbond_other 1.133 r_angle_other_deg 0.941 r_chiral_restr 0.133 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3071 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing