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Crystal structure of a formyltetrahydrofolate deformylase (PP_0327) from PSEUDOMONAS PUTIDA KT2440 at 2.25 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 277 0.1860M potassium fluoride 20.4000% polyethylene glycol 3350, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K 2 VAPOR DIFFUSION,SITTING DROP,NANODROP 8 277 10.0000% PEG-8000, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.213 α = 90 b = 93.965 β = 101.38 c = 97.129 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 325 mm CCD Flat mirror (vertical focusing) 2010-02-11 M MAD 2 1 x-ray 100 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2009-07-31 M MAD ,0.97908 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.95369 SSRL BL11-1 2 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97922,0.91837 SSRL BL9-2 ,0.97908
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 1,2 2.25 42.133 99.8 0.109 3.1 67847 41.528
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.25 42.133 67821 3426 99.77 0.225 0.222 0.274 0.2831 RANDOM 64.366
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] -0.57 -0.22 0.31 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.612 r_dihedral_angle_4_deg 16.156 r_dihedral_angle_3_deg 12.364 r_dihedral_angle_1_deg 5.809 r_angle_refined_deg 1.046 r_angle_other_deg 0.811 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.612 r_dihedral_angle_4_deg 16.156 r_dihedral_angle_3_deg 12.364 r_dihedral_angle_1_deg 5.809 r_angle_refined_deg 1.046 r_angle_other_deg 0.811 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8947 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing