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Crystal structure of GNP-bound YlqF from T. maritima
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 297 100mM HEPES (pH 7.5), 5% (v/v) isopropanol, 20% (w/v) polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.34 47.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.132 α = 90 b = 75.15 β = 90 c = 104.919 γ = 90
Symmetry Space Group P 21 21 21
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 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6C1 1.23985 PAL/PLS 6C1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 20 19460
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 19460
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 2 19.01 17410 1994 99.56 0.23309 0.22712 0.2844 0.258 RANDOM 34.761
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] 0.43 2.29 -2.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.899 r_dihedral_angle_3_deg 17.743 r_dihedral_angle_4_deg 14.484 r_dihedral_angle_1_deg 6.198 r_sphericity_free 4.302 r_scangle_it 3.329 r_scbond_it 2.486 r_rigid_bond_restr 2.215 r_sphericity_bonded 1.952 r_mcangle_it 1.707
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.899 r_dihedral_angle_3_deg 17.743 r_dihedral_angle_4_deg 14.484 r_dihedral_angle_1_deg 6.198 r_sphericity_free 4.302 r_scangle_it 3.329 r_scbond_it 2.486 r_rigid_bond_restr 2.215 r_sphericity_bonded 1.952 r_mcangle_it 1.707 r_angle_refined_deg 1.493 r_mcbond_it 1.027 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.19 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.103 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1873 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction