☰ Navigation Tabs
Crystal Structure of ORF 1438 a putative Glucose/ribitol dehydrogenase from Clostridium thermocellum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EDO PDB entry 1EDO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 HANGING DROP VAPOR DIFUSION USING
1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION
(9 MG/ML) AND A PRECIPITANT SOLUTION CONTAINING 0.1M AMMONIUM
DIHYDROGEN PHOSPHATE AND 20% W/V PEG 3350, SETUP AT 291K.
Crystal Properties Matthews coefficient Solvent content 2.59 52.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.982 α = 90 b = 99.487 β = 90 c = 69.833 γ = 90
Symmetry Space Group C 2 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 CCD MARMOSAIC 300 mm CCD Rosenbaum 2006-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.9790 APS 22-ID
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 1.9 20 92.68 0.053 21.2 6.6 20685 19128 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) 1.9 1.97 57.9 0.352 3.23 3.8 1282
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 Replacemet THROUGHOUT PDB entry 1EDO 1.9 20 19128 19128 1045 92.68 0.23321 0.23321 0.23235 0.2357 0.24902 0.2343 RANDOM 23.136
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] -1.36 1.9 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.909 r_dihedral_angle_3_deg 14.363 r_dihedral_angle_4_deg 11.654 r_dihedral_angle_1_deg 4.926 r_scangle_it 2.035 r_scbond_it 1.333 r_angle_refined_deg 1.054 r_mcangle_it 0.935 r_mcbond_it 0.542 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.909 r_dihedral_angle_3_deg 14.363 r_dihedral_angle_4_deg 11.654 r_dihedral_angle_1_deg 4.926 r_scangle_it 2.035 r_scbond_it 1.333 r_angle_refined_deg 1.054 r_mcangle_it 0.935 r_mcbond_it 0.542 r_nbtor_refined 0.294 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.151 r_symmetry_hbond_refined 0.121 r_xyhbond_nbd_refined 0.104 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 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 1548 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms
Software Software Software Name Purpose CCP4 model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing