1QWM

Structure of Helicobacter pylori catalase with formic acid bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QWLPDB entry 1QWL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629315% PEG MME 550, 0.1 M sodium citrate, 10 mM ZnSO4, 3 mM NaN3, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0540.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.756α = 90
b = 154.961β = 90
c = 96.163γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 42002-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9330ESRFID14-1

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
11.629.997.40.047124796118512
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6992.50.1798557

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 1QWL1.629.8812479611851262821000.1940.195550.193870.22695RANDOM15.149
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]
0.94-0.19-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.067
r_scangle_it3.54
r_scbond_it2.319
r_angle_refined_deg1.612
r_mcangle_it1.453
r_mcbond_it0.924
r_symmetry_hbond_refined0.239
r_nbd_refined0.213
r_symmetry_vdw_refined0.202
r_xyhbond_nbd_refined0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.067
r_scangle_it3.54
r_scbond_it2.319
r_angle_refined_deg1.612
r_mcangle_it1.453
r_mcbond_it0.924
r_symmetry_hbond_refined0.239
r_nbd_refined0.213
r_symmetry_vdw_refined0.202
r_xyhbond_nbd_refined0.15
r_chiral_restr0.118
r_bond_refined_d0.017
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8040
Nucleic Acid Atoms
Solvent Atoms933
Heterogen Atoms197

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing