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Domain shifting confirms monomeric structure of Escherichia sugar phosphatase SUPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RLM PDB ENTRY 1RLM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 290 20% PEG8000, 0.1 M SODIUM PHOSPHATE-CITRATE, 10% GLYCEROL, pH 4.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.21 44.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.774 α = 90 b = 111.295 β = 106.23 c = 68.802 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 IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2006-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 50 95.6 0.056 0.056 13.4 7 42397 42397
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 73.6 0.323 0.358 3.6 4.7
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 (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 1RLM 1.9 20 40958 40958 1329 95.69 0.2116 0.2058 0.20427 0.2097 0.25188 0.2588 RANDOM 35.808
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] -0.16 0.04 0.29 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.012 r_dihedral_angle_4_deg 15.766 r_dihedral_angle_3_deg 15.41 r_scangle_it 8.931 r_scbond_it 6.573 r_dihedral_angle_1_deg 5.871 r_mcangle_it 4.862 r_mcbond_it 3.868 r_angle_refined_deg 1.41 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.012 r_dihedral_angle_4_deg 15.766 r_dihedral_angle_3_deg 15.41 r_scangle_it 8.931 r_scbond_it 6.573 r_dihedral_angle_1_deg 5.871 r_mcangle_it 4.862 r_mcbond_it 3.868 r_angle_refined_deg 1.41 r_nbtor_refined 0.298 r_xyhbond_nbd_refined 0.278 r_symmetry_hbond_refined 0.196 r_symmetry_vdw_refined 0.171 r_nbd_refined 0.161 r_chiral_restr 0.096 r_bond_refined_d 0.023 r_gen_planes_refined 0.005 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 4248 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement