4PTK

Crystal structure of Staphylococcal IMPase-I complex with 3Mg2+ and Phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QMF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82980.2M MgCl2, 0.1M HEPES pH8,18% (W/V) PEG 3350, Soaked with 0.1M HEPES pH8, 18% (W/V) PEG 3350, 10% Glycerol for 24 hours, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1242.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.428α = 90
b = 62.455β = 90
c = 140.497γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrorMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.503140.49797.30.14914.37.61841118411
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.5032.6495.70.6950.6950.2661.17.72588

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 REPLACEMENTTHROUGHOUT3QMF2.50346.721838795396.750.1810.17710.2569RANDOM27.592
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]
0.060.89-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.309
r_dihedral_angle_4_deg28.816
r_dihedral_angle_3_deg19.581
r_dihedral_angle_1_deg7.735
r_angle_refined_deg1.807
r_angle_other_deg0.869
r_chiral_restr0.096
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.309
r_dihedral_angle_4_deg28.816
r_dihedral_angle_3_deg19.581
r_dihedral_angle_1_deg7.735
r_angle_refined_deg1.807
r_angle_other_deg0.869
r_chiral_restr0.096
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4191
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms28

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
XDSdata reduction