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crystal structure of sulfur-free 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 3.42 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.25 α = 90 b = 160.25 β = 90 c = 170.821 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 MARMOSAIC 225 mm CCD 2008-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 46.414 100 0.1 20.9 14.6 51064
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 0.536 0.536 5.3 14.6
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 FOURIER SYNTHESIS THROUGHOUT 2.4 46.41 48445 2578 100 0.16715 0.16471 0.1771 0.21381 0.2261 RANDOM 29.396
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] -1.68 -0.84 -1.68 2.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.618 r_dihedral_angle_4_deg 19.492 r_dihedral_angle_3_deg 16.293 r_dihedral_angle_1_deg 6.494 r_scangle_it 4.118 r_scbond_it 2.675 r_angle_refined_deg 1.695 r_mcangle_it 1.563 r_mcbond_it 0.841 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.618 r_dihedral_angle_4_deg 19.492 r_dihedral_angle_3_deg 16.293 r_dihedral_angle_1_deg 6.494 r_scangle_it 4.118 r_scbond_it 2.675 r_angle_refined_deg 1.695 r_mcangle_it 1.563 r_mcbond_it 0.841 r_chiral_restr 0.113 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 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 6507 Nucleic Acid Atoms Solvent Atoms 431 Heterogen Atoms 45
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MxCuBE data collection MOSFLM data reduction REFMAC phasing