1QWS

Structure of the D181N variant of catalase HPII from E. coli


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GGEPDB ENTRY 1GGE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP929315% PEG 3350, 1.6M LiCl, 0.1M Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1241.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.434α = 90
b = 132.881β = 109.66
c = 122.098γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.9763ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.927.8199.50.0977.2218818218251
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.91.9997.315850

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1GGE1.928218818207829109891000.16450.167270.164460.22046RANDOM20.472
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]
-0.340.56-0.270.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.53
r_scangle_it3.74
r_scbond_it2.504
r_angle_refined_deg1.634
r_mcangle_it1.536
r_mcbond_it0.914
r_symmetry_hbond_refined0.336
r_symmetry_vdw_refined0.221
r_nbd_refined0.215
r_xyhbond_nbd_refined0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.53
r_scangle_it3.74
r_scbond_it2.504
r_angle_refined_deg1.634
r_mcangle_it1.536
r_mcbond_it0.914
r_symmetry_hbond_refined0.336
r_symmetry_vdw_refined0.221
r_nbd_refined0.215
r_xyhbond_nbd_refined0.17
r_chiral_restr0.128
r_bond_refined_d0.019
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms23025
Nucleic Acid Atoms
Solvent Atoms3033
Heterogen Atoms172

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing