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Crystal structure of NTF2-like protein of unknown function (YP_680363.1) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 1.45 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2000M NaOAc, 30.0000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.21 44.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.64 α = 90 b = 57.64 β = 90 c = 59.39 γ = 120
Symmetry Space Group P 32 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 MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2008-08-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97939,0.97925 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 1.45 25.933 99.7 0.043 16.58 7.16 20633 -3 17.008
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 1.45 1.5 98.8 0.538 2.5
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 1.45 25.933 20606 1054 99.85 0.171 0.171 0.178 0.181 0.1858 RANDOM 20.996
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] 0.08 0.04 0.08 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.662 r_dihedral_angle_4_deg 30.342 r_dihedral_angle_3_deg 10.53 r_scangle_it 6.442 r_dihedral_angle_1_deg 5.841 r_scbond_it 5.369 r_mcangle_it 2.69 r_mcbond_it 2.148 r_angle_refined_deg 1.753 r_angle_other_deg 1.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.662 r_dihedral_angle_4_deg 30.342 r_dihedral_angle_3_deg 10.53 r_scangle_it 6.442 r_dihedral_angle_1_deg 5.841 r_scbond_it 5.369 r_mcangle_it 2.69 r_mcbond_it 2.148 r_angle_refined_deg 1.753 r_angle_other_deg 1.033 r_mcbond_other 0.503 r_nbd_refined 0.285 r_symmetry_vdw_other 0.277 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.184 r_nbd_other 0.182 r_symmetry_hbond_refined 0.182 r_symmetry_vdw_refined 0.12 r_chiral_restr 0.088 r_nbtor_other 0.088 r_xyhbond_nbd_other 0.065 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 873 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 18
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