3QGK

3.0 A Model of Iron Containing Urease UreA2B2 from Helicobacter mustelae (refined w/ no ordered solvent)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.42936.7 mg/ml protein, 6.7 mM Tris, 20% MPD, 0.07 M sodium acetate, 0.013 M calcium chloride, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.5465.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 166.98α = 90
b = 223.94β = 90
c = 395.87γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-09-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.3ALS5.0.3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.99867.29298.60.2010.2019.38.8145678145678-359.84
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.1694.30.8090.8090.95.120140

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 1EJX367.2914535514535572830.17810.17810.17710.1965RANDOM31.4444
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]
0.6436-2.17711.5334
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion20.33
t_omega_torsion2.7
t_improper_torsion1.246
t_angle_deg1.17
t_gen_planes0.0141
t_bond_d0.0088
t_trig_c_planes0.0072
t_dihedral_angle_d
t_it
t_nbd
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion20.33
t_omega_torsion2.7
t_improper_torsion1.246
t_angle_deg1.17
t_gen_planes0.0141
t_bond_d0.0088
t_trig_c_planes0.0072
t_dihedral_angle_d
t_it
t_nbd
t_chiral_improper_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms36408
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms12

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
BOSdata collection
BUSTERrefinement