☰ Navigation Tabs
Crystal structure of the pED208 TraM N-terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CMB PDB ENTRY 1CMB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 5% PEG 4000, 50mM MES, 5mM magnesium sulphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 39.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.069 α = 90 b = 54.069 β = 90 c = 67.268 γ = 90
Symmetry Space Group P 41 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 ADSC QUANTUM 315r 2008-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1158 ALS 8.3.1
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 1.3 50 81 0.044 39.2 7.5 25197 25159 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.35 100 0.329 6.6 7.4 2459
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1CMB 1.3 42.14 23875 1284 99.85 0.15092 0.14977 0.1639 0.17293 0.1768 RANDOM 9.999
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] 0.21 0.21 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.436 r_dihedral_angle_4_deg 26.299 r_dihedral_angle_3_deg 11.259 r_dihedral_angle_1_deg 4.649 r_scangle_it 4.595 r_scbond_it 2.97 r_mcangle_it 1.999 r_angle_refined_deg 1.38 r_rigid_bond_restr 1.332 r_mcbond_it 1.201
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.436 r_dihedral_angle_4_deg 26.299 r_dihedral_angle_3_deg 11.259 r_dihedral_angle_1_deg 4.649 r_scangle_it 4.595 r_scbond_it 2.97 r_mcangle_it 1.999 r_angle_refined_deg 1.38 r_rigid_bond_restr 1.332 r_mcbond_it 1.201 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 805 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 7
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling