X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PG4pdb entry 1PG4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52876-15% PEG 8000, 9-13% ethylene glycol, 50 mM BTP, 1 mM CoA, 1 mM Acetate, 1 mM AMP, 1 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties
Matthews coefficientSolvent content
2.4249.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.906α = 90
b = 94.933β = 90
c = 161.814γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDCUSTOM-MADE2003-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C0.95NSLSX12C

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
12.5881.6598.90.07210.85.14207938.3
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)
12.582.71000.2241

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTpdb entry 1PG42.5881.6542079226198.970.1860.1830.247RANDOM18.048
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]
0.71-1.140.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.148
r_dihedral_angle_4_deg20.21
r_dihedral_angle_3_deg15.837
r_dihedral_angle_1_deg6.416
r_scangle_it2.681
r_scbond_it1.672
r_angle_refined_deg1.532
r_mcangle_it1.019
r_mcbond_it0.611
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.148
r_dihedral_angle_4_deg20.21
r_dihedral_angle_3_deg15.837
r_dihedral_angle_1_deg6.416
r_scangle_it2.681
r_scbond_it1.672
r_angle_refined_deg1.532
r_mcangle_it1.019
r_mcbond_it0.611
r_nbtor_refined0.31
r_nbd_refined0.211
r_symmetry_vdw_refined0.179
r_symmetry_hbond_refined0.148
r_xyhbond_nbd_refined0.142
r_chiral_restr0.096
r_bond_refined_d0.014
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9828
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms150

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing