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Crystal structure of functional region of UafA from Staphylococcus saprophyticus in P212121 form
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 22.5% PEG 3350, 130mM tri-ammonium citrate, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.78 55.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.814 α = 90 b = 73.609 β = 90 c = 110.965 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 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 1.7 50 99.3 0.048 7.3 58776
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 1.7 1.76 94.9 0.408 6.5 5548
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3IS1 1.7 19.56 52901 5764 99.31 0.19315 0.1906 0.2164 0.1944 RANDOM 26.939
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 35.694 r_dihedral_angle_4_deg 16.001 r_dihedral_angle_3_deg 13.74 r_dihedral_angle_1_deg 6.325 r_scangle_it 3.257 r_scbond_it 2.089 r_angle_refined_deg 1.366 r_mcangle_it 1.261 r_mcbond_it 0.753 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.694 r_dihedral_angle_4_deg 16.001 r_dihedral_angle_3_deg 13.74 r_dihedral_angle_1_deg 6.325 r_scangle_it 3.257 r_scbond_it 2.089 r_angle_refined_deg 1.366 r_mcangle_it 1.261 r_mcbond_it 0.753 r_nbtor_refined 0.311 r_nbd_refined 0.194 r_symmetry_hbond_refined 0.18 r_symmetry_vdw_refined 0.163 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 3121 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 6
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling