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Crystal structure of functional region of UafA from Staphylococcus saprophyticus at 1.50 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IS1 PDB ENTRY 3IS1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 30% PEG MME2000, 70mM potassium thiocyanate, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.935 α = 90 b = 126.926 β = 96.75 c = 45.83 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 225 mm CCD 2008-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00000 SPring-8 BL41XU
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 1.5 50 99.9 0.048 3.8 68192
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 1.5 1.55 100 0.149 3.7 6814
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3IS1 1.5 19.18 61383 6704 99.9 0.16745 0.1654 0.1675 0.18602 0.1629 RANDOM 11.662
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.315 r_dihedral_angle_4_deg 13.681 r_dihedral_angle_3_deg 11.757 r_dihedral_angle_1_deg 6.313 r_scangle_it 2.77 r_scbond_it 1.812 r_angle_refined_deg 1.186 r_mcangle_it 1.077 r_mcbond_it 0.578 r_metal_ion_refined 0.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.315 r_dihedral_angle_4_deg 13.681 r_dihedral_angle_3_deg 11.757 r_dihedral_angle_1_deg 6.313 r_scangle_it 2.77 r_scbond_it 1.812 r_angle_refined_deg 1.186 r_mcangle_it 1.077 r_mcbond_it 0.578 r_metal_ion_refined 0.344 r_nbtor_refined 0.309 r_nbd_refined 0.23 r_symmetry_vdw_refined 0.198 r_symmetry_hbond_refined 0.113 r_xyhbond_nbd_refined 0.097 r_chiral_restr 0.08 r_bond_refined_d 0.008 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_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 3267 Nucleic Acid Atoms Solvent Atoms 526 Heterogen Atoms 17
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling