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Crystal structure of YnjE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 17-21% PEG 4000, 0.1 M sodium phosphate citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.51 64.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.949 α = 90 b = 160.949 β = 90 c = 173.992 γ = 120
Symmetry Space Group P 63 2 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 MAR CCD 165 mm 2008-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.8 ESRF BM14
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 2.4 40.996 100 0.112 0.112 25.7 21.8 52432
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) 1 2.4 2.53 100 0.551 0.551 6.4 21.5
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 SAD THROUGHOUT 2.4 40.996 49744 2653 100 0.16121 0.15862 0.1646 0.21112 0.2175 RANDOM 35.274
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] 0.26 0.13 0.26 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.767 r_dihedral_angle_4_deg 17.737 r_dihedral_angle_3_deg 15.405 r_dihedral_angle_1_deg 6.186 r_scangle_it 3.88 r_scbond_it 2.502 r_angle_refined_deg 1.601 r_mcangle_it 1.424 r_mcbond_it 0.753 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.767 r_dihedral_angle_4_deg 17.737 r_dihedral_angle_3_deg 15.405 r_dihedral_angle_1_deg 6.186 r_scangle_it 3.88 r_scbond_it 2.502 r_angle_refined_deg 1.601 r_mcangle_it 1.424 r_mcbond_it 0.753 r_chiral_restr 0.1 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6509 Nucleic Acid Atoms Solvent Atoms 560 Heterogen Atoms 50
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MxCuBE data collection MOSFLM data reduction SHARP phasing