5MP7 | pdb_00005mp7

Crystal structure of phosphoribosylpyrophosphate synthetase from Mycobacterium smegmatis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DKR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.6277.150.2M NaCl, 0.1M Sodium acetate, 30% (v/v) 2-Methyl-2,4-pentanediol
Crystal Properties
Matthews coefficientSolvent content
2.3347.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.292α = 90
b = 85.292β = 90
c = 249.791γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.98ESRFID23-1

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
12.443.3896.180.0676.241.93572338.07
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)
12.42.4997.260.342.341.9

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1DKR2.450.0133860182096.190.19960.198170.210.22550.23RANDOM42.983
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]
-2.53-2.535.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.107
r_dihedral_angle_4_deg19.278
r_dihedral_angle_3_deg16.216
r_long_range_B_refined12.159
r_long_range_B_other12.159
r_scangle_other8.146
r_dihedral_angle_1_deg6.186
r_scbond_it5.047
r_scbond_other5.047
r_mcangle_it4.831
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6864
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing