1ZT9 | pdb_00001zt9

E. coli trp repressor, tetragonal crystal form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WRPPDB ENTRY 2WRP, BIOLOGICAL UNIT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.62942.8 M ammonium sulfate plus 50 mM sodium, potassium phosphate buffer, 5 mM L-tryptophan, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 5.60
Crystal Properties
Matthews coefficientSolvent content
3.160.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.348α = 90
b = 81.348β = 90
c = 72.687γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MIRRORS2003-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X26CNSLSX26C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
125099.10.0634.331825-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.070.1693.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)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 2WRP, BIOLOGICAL UNIT230-330461301661636990.1670.1640.180.2190.23RANDOM19.83
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]
0.080.08-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it6.149
r_dihedral_angle_1_deg4.673
r_scbond_it4.331
r_mcangle_it4.283
r_mcbond_it2.948
r_angle_refined_deg1.203
r_angle_other_deg0.802
r_nbd_other0.236
r_symmetry_vdw_other0.23
r_symmetry_vdw_refined0.212
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it6.149
r_dihedral_angle_1_deg4.673
r_scbond_it4.331
r_mcangle_it4.283
r_mcbond_it2.948
r_angle_refined_deg1.203
r_angle_other_deg0.802
r_nbd_other0.236
r_symmetry_vdw_other0.23
r_symmetry_vdw_refined0.212
r_nbd_refined0.208
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.164
r_nbtor_other0.08
r_chiral_restr0.069
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3248
Nucleic Acid Atoms
Solvent Atoms558
Heterogen Atoms100

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection