1W8G | pdb_00001w8g

CRYSTAL STRUCTURE OF E. COLI K-12 YGGS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B54PDB ENTRY 1B54

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1620% PEG 4000, 16% ISOPROPANOL, 0.1 M NA-CITRATE BUFFER PH 6, 5% SODIUM DEXTRANE SULPHATE
Crystal Properties
Matthews coefficientSolvent content
3.160

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.017α = 90
b = 124.017β = 90
c = 83.729γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2003-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
123999.90.050.0534.292229525.32
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.051000.340.345.99.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1B542392106412221000.1630.1610.170.1950.2RANDOM21.57
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]
0.280.28-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.179
r_dihedral_angle_4_deg18.107
r_dihedral_angle_3_deg14.153
r_dihedral_angle_1_deg5.261
r_scangle_it2.337
r_scbond_it1.557
r_angle_refined_deg1.119
r_mcangle_it0.876
r_mcbond_it0.819
r_angle_other_deg0.774
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.179
r_dihedral_angle_4_deg18.107
r_dihedral_angle_3_deg14.153
r_dihedral_angle_1_deg5.261
r_scangle_it2.337
r_scbond_it1.557
r_angle_refined_deg1.119
r_mcangle_it0.876
r_mcbond_it0.819
r_angle_other_deg0.774
r_symmetry_vdw_other0.236
r_nbd_refined0.208
r_symmetry_hbond_refined0.197
r_symmetry_vdw_refined0.187
r_nbd_other0.186
r_xyhbond_nbd_refined0.173
r_nbtor_refined0.166
r_nbtor_other0.082
r_chiral_restr0.062
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1740
Nucleic Acid Atoms
Solvent Atoms274
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing