2P1Z | pdb_00002p1z

Crystal structure of phosphoribosyltransferase from Corynebacterium diphtheriae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52890.2 M Magnesium chloride, 0.1 M Tris-HCl, 25 % PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
1.9235.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.438α = 90
b = 103.709β = 90
c = 39.417γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-08-14MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97929, 0.97943APS19-ID

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
12.255087.50.08232.537.51474012900-3
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)
12.252.3340.90.5221.763.4591

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.4439.41107451074554297.680.22970.22970.225770.22690.308470.3102RANDOM57.577
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]
-4.492.971.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.149
r_dihedral_angle_3_deg19.595
r_dihedral_angle_4_deg16.017
r_dihedral_angle_1_deg6.142
r_scangle_it2.315
r_scbond_it1.451
r_angle_refined_deg1.389
r_mcangle_it1.036
r_mcbond_it0.673
r_nbtor_refined0.296
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2410
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing