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Crystal structure of a Putative phosphoribosylformylglycinamidine cyclo-ligase (BDI_2101) from Parabacteroides distasonis ATCC 8503 at 1.91 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.33 277 34.0000% polyethylene glycol 300, 0.3000M calcium acetate, 0.1M sodium cacodylate pH 6.33, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.36 47.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.945 α = 90 b = 99.945 β = 90 c = 163.02 γ = 90
Symmetry Space Group P 41 21 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 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2009-11-06 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97949 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.91 29.623 99.7 0.074 13.15 64592 -3 25.989
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 1.91 1.98 99.7 0.71 2
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 1.91 29.623 64507 3265 99.83 0.156 0.154 0.1667 0.19 0.1974 RANDOM 28.322
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] 1.01 1.01 -2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.428 r_dihedral_angle_4_deg 18.463 r_dihedral_angle_3_deg 13.621 r_scangle_it 6.709 r_dihedral_angle_1_deg 5.814 r_scbond_it 4.68 r_mcangle_it 2.788 r_mcbond_it 1.705 r_angle_refined_deg 1.529 r_angle_other_deg 1.195
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.428 r_dihedral_angle_4_deg 18.463 r_dihedral_angle_3_deg 13.621 r_scangle_it 6.709 r_dihedral_angle_1_deg 5.814 r_scbond_it 4.68 r_mcangle_it 2.788 r_mcbond_it 1.705 r_angle_refined_deg 1.529 r_angle_other_deg 1.195 r_mcbond_other 0.516 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5529 Nucleic Acid Atoms Solvent Atoms 459 Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing