2IQF

Crystal structure of Helicobacter pylori catalase compound I


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 MME550, 0.1M Sodium citrate, 10mM ZnSO4, 3mM Sodium azide, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0239.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.385α = 90
b = 154.286β = 90
c = 95.808γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.97950ESRFID14-1

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
11.863797.40.0846.44.180997741353
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)
1.861.9597.40.41.53.711375

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1QWL1.863774135392896.40.150510.148470.18845RANDOM13.633
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]
0.64-0.32-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.846
r_dihedral_angle_4_deg18.539
r_dihedral_angle_3_deg14.184
r_dihedral_angle_1_deg6.302
r_scangle_it2.625
r_scbond_it1.931
r_angle_refined_deg1.555
r_angle_other_deg1.394
r_mcangle_it1.153
r_mcbond_it1.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.846
r_dihedral_angle_4_deg18.539
r_dihedral_angle_3_deg14.184
r_dihedral_angle_1_deg6.302
r_scangle_it2.625
r_scbond_it1.931
r_angle_refined_deg1.555
r_angle_other_deg1.394
r_mcangle_it1.153
r_mcbond_it1.007
r_symmetry_vdw_other0.251
r_mcbond_other0.209
r_nbd_refined0.206
r_nbd_other0.203
r_symmetry_hbond_refined0.19
r_symmetry_vdw_refined0.186
r_nbtor_refined0.184
r_xyhbond_nbd_refined0.157
r_chiral_restr0.108
r_nbtor_other0.089
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8135
Nucleic Acid Atoms
Solvent Atoms884
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing