☰ Navigation Tabs
X-ray structure of galt-like protein from arabidopsis thaliana at5g18200
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VKV PDB ENTRY 1VKV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 293 10 MG/ML PROTEIN, 20% PEG 2000, 0.2M Sodium Chloride, 0.10M MES-Acetate, vapor diffusion, hanging drop, temperature 293K, pH 5.50
Crystal Properties Matthews coefficient Solvent content 2.4 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.037 α = 90 b = 95.65 β = 90 c = 110.918 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 APS-1 SAGITALLY FOCUSING 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR 2004-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
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 1.834 34.486 96.5 0.083 15.249 6.9 57501
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) 1.83 1.9 71.4 0.386 4.543 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1VKV 1.83 31.28 54539 2903 98.1 0.18833 0.186 0.231 0.2303 RANDOM 24.85
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.991 r_dihedral_angle_4_deg 23.577 r_dihedral_angle_3_deg 13.334 r_dihedral_angle_1_deg 6.304 r_scangle_it 3.653 r_scbond_it 2.545 r_angle_refined_deg 1.558 r_mcangle_it 1.539 r_mcbond_it 0.932 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.991 r_dihedral_angle_4_deg 23.577 r_dihedral_angle_3_deg 13.334 r_dihedral_angle_1_deg 6.304 r_scangle_it 3.653 r_scbond_it 2.545 r_angle_refined_deg 1.558 r_mcangle_it 1.539 r_mcbond_it 0.932 r_nbtor_refined 0.307 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.207 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.107 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_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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4884 Nucleic Acid Atoms Solvent Atoms 500 Heterogen Atoms 72
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement