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Crystal structure of a formyltetrahydrofolate deformylase (purU, PP_1943) from PSEUDOMONAS PUTIDA KT2440 at 2.05 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 277 1.0000M NaCitrate, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.43 49.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.452 α = 90 b = 118.245 β = 90 c = 129.193 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 325 mm CCD Flat collimating mirror, toroid focusing mirror 2009-07-30 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97925,0.97911 SSRL BL9-2
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 2.05 29.961 99.8 0.143 0.143 8.1 3.7 79699 24.029
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) 2.05 2.1 100 0.804 0.804 1.6 3.7 5863
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.05 29.961 79629 3987 99.71 0.187 0.184 0.1889 0.24 0.2426 RANDOM 28.05
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] 0.69 -1.04 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.278 r_dihedral_angle_4_deg 17.972 r_dihedral_angle_3_deg 14.245 r_scangle_it 7.051 r_dihedral_angle_1_deg 6.957 r_scbond_it 5.361 r_mcangle_it 3.216 r_mcbond_it 2.022 r_angle_refined_deg 1.583 r_angle_other_deg 0.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.278 r_dihedral_angle_4_deg 17.972 r_dihedral_angle_3_deg 14.245 r_scangle_it 7.051 r_dihedral_angle_1_deg 6.957 r_scbond_it 5.361 r_mcangle_it 3.216 r_mcbond_it 2.022 r_angle_refined_deg 1.583 r_angle_other_deg 0.924 r_mcbond_other 0.58 r_chiral_restr 0.096 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8777 Nucleic Acid Atoms Solvent Atoms 785 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement PHENIX refinement MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction HELXD phasing autoSHARP phasing