2WLT

The crystal structure of Helicobacter pylori L-asparaginase at 1.4 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17PROTEIN WAS CRYSTALLIZED FROM 17.5% W/V PEG 4000, 0.1 M MG FORMATE, 0.1 M HEPES-NAOH, PH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.141

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.559α = 90
b = 94.796β = 90
c = 100.342γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH SX-1652007-08-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
11.42099.70.122.87.159013-3
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)
11.41.4299.10.277.28.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPDB ENTRY 1WSA1.42058995293999.50.12640.13120.1687RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
2780.35
RMS Deviations
KeyRefinement Restraint Deviation
s_non_zero_chiral_vol0.796
s_anti_bump_dis_restr0.41
s_approx_iso_adps0.094
s_zero_chiral_vol0.066
s_similar_adp_cmpnt0.055
s_angle_d0.032
s_from_restr_planes0.0307
s_bond_d0.012
s_rigid_bond_adp_cmpnt0.004
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2448
Nucleic Acid Atoms
Solvent Atoms391
Heterogen Atoms9

Software

Software
Software NamePurpose
SHELXL-97refinement
HKLdata reduction
HKLdata scaling
PHASERphasing