2VHE | pdb_00002vhe

PglD-CoA complex: An acetyl transferase from Campylobacter jejuni


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NPOPDB ENTRY 2NPO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1 M SODIUM CITRATE PH 5.6, 0.16 M SODIUM TARTRATE AND 2.0 M AMMONIUM SULFATE
Crystal Properties
Matthews coefficientSolvent content
3.2361.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.25α = 90
b = 99.25β = 90
c = 143.027γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-09-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.8151000.0711.43.248692
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)
11.81.91000.462.43.2

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 Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2NPO1.8154615124571000.1910.190.190.225RANDOM26.77
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]
-0.09-0.04-0.090.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.852
r_dihedral_angle_3_deg14.335
r_dihedral_angle_4_deg10.317
r_dihedral_angle_1_deg8.424
r_scangle_it3.417
r_scbond_it2.289
r_angle_refined_deg1.604
r_mcangle_it1.341
r_mcbond_it0.88
r_nbtor_refined0.307
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2810
Nucleic Acid Atoms
Solvent Atoms263
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing