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X-ray structure of protein from Arabidopsis thaliana AT1G79260
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 10 MG/ML PROTEIN, 18% PEG2K, 0.025 M TRIS, pH 8.0, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.4 48.5 2.4 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.056 α = 90 b = 80.026 β = 90 c = 36.886 γ = 90
Symmetry Space Group P 21 21 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 300 mm CCD HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR 2005-06-13 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 300 mm CCD HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR 2005-06-13 M MAD 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID 2 SYNCHROTRON APS BEAMLINE 22-ID 0.97934, 0.96863 APS 22-ID
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 1,2 1.31 50 96.3 0.066 14.91 7.5 41019
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) 1.31 1.34 93.1 93.1 0.24 6.178 6.8
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 (All) 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 1.32 48.06 38582 2068 95.4 0.157 0.15708 0.156 0.1538 0.186 0.1842 RANDOM 17.287
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] 0.07 -0.1 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.693 r_dihedral_angle_4_deg 18.235 r_dihedral_angle_3_deg 11.941 r_dihedral_angle_1_deg 6.37 r_scangle_it 3.552 r_sphericity_free 3.111 r_sphericity_bonded 3.071 r_scbond_it 2.751 r_rigid_bond_restr 2.309 r_mcangle_it 1.834
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.693 r_dihedral_angle_4_deg 18.235 r_dihedral_angle_3_deg 11.941 r_dihedral_angle_1_deg 6.37 r_scangle_it 3.552 r_sphericity_free 3.111 r_sphericity_bonded 3.071 r_scbond_it 2.751 r_rigid_bond_restr 2.309 r_mcangle_it 1.834 r_mcbond_it 1.329 r_angle_refined_deg 1.311 r_nbtor_refined 0.292 r_nbd_refined 0.192 r_xyhbond_nbd_refined 0.179 r_symmetry_vdw_refined 0.16 r_symmetry_hbond_refined 0.109 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1220 Nucleic Acid Atoms Solvent Atoms 329 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SOLOMON phasing ARP/wARP model building