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Crystal structure of a putative NTP pyrophosphohydrolase (Exig_1061) from EXIGUOBACTERIUM SP. 255-15 at 1.78 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 277 1.4000M Na3Citrate, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.16 43.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.088 α = 90 b = 69.043 β = 111.81 c = 50.208 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 315 2007-08-30 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0000,0.9798 ALS 8.2.2
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 1.78 39.621 98.1 0.069 0.069 9.8 2.8 15531 21.33
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) 2 2.05 99.9 0.943 2.4
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 1.78 39.62 15531 788 97.8 0.179 0.177 0.1841 0.222 0.2305 RANDOM 26.66
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] 2.57 0.82 -0.84 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.624 r_dihedral_angle_4_deg 22.22 r_dihedral_angle_3_deg 12.438 r_scangle_it 7.658 r_scbond_it 5.037 r_dihedral_angle_1_deg 4.881 r_mcangle_it 2.904 r_mcbond_it 1.768 r_angle_refined_deg 1.298 r_angle_other_deg 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.624 r_dihedral_angle_4_deg 22.22 r_dihedral_angle_3_deg 12.438 r_scangle_it 7.658 r_scbond_it 5.037 r_dihedral_angle_1_deg 4.881 r_mcangle_it 2.904 r_mcbond_it 1.768 r_angle_refined_deg 1.298 r_angle_other_deg 0.85 r_mcbond_other 0.485 r_chiral_restr 0.08 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1321 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 8
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