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structure of human ECE-1 complexed with phosphoramidon
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DMT PDB ENTRY 1DMT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 294 30% Jeffamine D2001, 0.1M bis Tris, pH 6.0, VAPOR DIFFUSION, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.65 53.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.88 α = 90 b = 120.88 β = 90 c = 192.346 γ = 120
Symmetry Space Group P 61 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2005-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.5418
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 2.38 20 98.7 0.07 13.7 34099 33656 1 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DMT 2.38 20 31886 31886 1705 99.05 0.26627 0.26627 0.26216 0.2511 0.34506 0.3237 RANDOM 45.686
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] 0.91 0.45 0.91 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.778 r_dihedral_angle_3_deg 19.287 r_dihedral_angle_4_deg 16.46 r_dihedral_angle_1_deg 6.797 r_scangle_it 2.151 r_angle_refined_deg 1.525 r_scbond_it 1.435 r_mcangle_it 1.048 r_angle_other_deg 0.893 r_mcbond_it 0.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.778 r_dihedral_angle_3_deg 19.287 r_dihedral_angle_4_deg 16.46 r_dihedral_angle_1_deg 6.797 r_scangle_it 2.151 r_angle_refined_deg 1.525 r_scbond_it 1.435 r_mcangle_it 1.048 r_angle_other_deg 0.893 r_mcbond_it 0.893 r_symmetry_hbond_refined 0.374 r_metal_ion_refined 0.272 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.195 r_symmetry_vdw_other 0.195 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.19 r_nbd_other 0.183 r_mcbond_other 0.126 r_xyhbond_nbd_other 0.116 r_chiral_restr 0.09 r_nbtor_other 0.088 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5305 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling SHARP phasing