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Crystal structure of Putative protoporphyrinogen oxidase (YP_001813199.1) from Exiguobacterium sp. 255-15 at 2.06 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2000M sodium acetate, 30.0000% polyethylene glycol 4000, 0.1M TRIS pH 8.5, Additive: 0.003 M flavin adenine dinucleotide (FAD), 0.003 M nicotinamide adenine dinucleotide (NAD), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.79 55.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.542 α = 90 b = 74.542 β = 90 c = 212.559 γ = 90
Symmetry Space Group P 43 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 mirror (vertical focusing) 2009-12-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97894,0.91837,0.97916 SSRL BL11-1
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 2.06 43.27 99.4 0.126 12.9 7.08 37840 -3 34.495
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 2.06 2.13 95.1 1.04 1.8 6.45
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 2.06 43.27 37781 1889 99.56 0.199 0.197 0.1981 0.241 0.2396 RANDOM 29.774
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] -0.12 -0.12 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.681 r_dihedral_angle_4_deg 16.451 r_dihedral_angle_3_deg 14.125 r_scangle_it 7.126 r_dihedral_angle_1_deg 5.967 r_scbond_it 5.242 r_mcangle_it 3.124 r_mcbond_it 1.911 r_angle_refined_deg 1.566 r_angle_other_deg 0.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.681 r_dihedral_angle_4_deg 16.451 r_dihedral_angle_3_deg 14.125 r_scangle_it 7.126 r_dihedral_angle_1_deg 5.967 r_scbond_it 5.242 r_mcangle_it 3.124 r_mcbond_it 1.911 r_angle_refined_deg 1.566 r_angle_other_deg 0.932 r_mcbond_other 0.524 r_chiral_restr 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3484 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 53
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