X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PT7apo-enzyme

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.5298PEG600, cacodylate, acetylCoA, pH 6.5, VAPOR DIFFUSION, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
4.1670.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.882α = 90
b = 146.882β = 90
c = 129.515γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-09-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9330ESRFID14-4

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
1220990.07876.510573210573222
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.1197.50.265

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTapo-enzyme220210573296936879599.080.15920.15920.157690.17598RANDOM23.857
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]
-1.38-0.69-1.382.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.367
r_scangle_it4.373
r_scbond_it2.644
r_mcangle_it1.535
r_angle_refined_deg1.498
r_mcbond_it0.785
r_nbd_refined0.204
r_symmetry_vdw_refined0.197
r_symmetry_hbond_refined0.193
r_xyhbond_nbd_refined0.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.367
r_scangle_it4.373
r_scbond_it2.644
r_mcangle_it1.535
r_angle_refined_deg1.498
r_mcbond_it0.785
r_nbd_refined0.204
r_symmetry_vdw_refined0.197
r_symmetry_hbond_refined0.193
r_xyhbond_nbd_refined0.144
r_chiral_restr0.106
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6432
Nucleic Acid Atoms
Solvent Atoms617
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
CCP4data scaling
AMoREphasing