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Crystal structure of a TRAP periplasmic solute binding protein from Rhodoferax ferrireducens (Rfer_1840), Target EFI-510211, with bound malonate, space group I422
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MCO PDB ENTRY 4MCO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 50 mg/mL protein in 10 mM HEPES, pH 7.5, 10 mM malonate, reservoir (MCSG4 C1): 0.1 M Bis-Tris Propane, pH 7.0, 2 M diammonium hydrogen citrate, cryoprotection: 4:1 2.5 M diammonium hydrogen citrate:reservoir, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.91 57.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.947 α = 90 b = 129.947 β = 90 c = 104.272 γ = 90
Symmetry Space Group I 4 2 2
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 2013-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54
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 1.8 100 99 0.085 0.085 8.6 4.9 41044 41044 20.4
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 1.8 1.83 100 0.658 4.5 2058
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 4MCO 1.8 23.509 40419 40419 1988 97.52 0.1443 0.1443 0.1428 0.1466 0.172 0.179 RANDOM 25.9372
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 f_dihedral_angle_d 14.177 f_angle_d 1.259 f_chiral_restr 0.07 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2380 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 20
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-3000 data reduction HKL-3000 data scaling AMoRE phasing