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 Propyl-AMP, 1 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties
Matthews coefficientSolvent content
2.550.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.05α = 90
b = 95.532β = 90
c = 164.25γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDADSC QUANTUM 2102005-07-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F20.97930CHESSF2

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
12.45093.40.10683.155167
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)
12.42.4982.90.372.44827

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1PG42.423552215265594.180.1880.1840.245RANDOM25.887
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]
-0.24-0.670.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.862
r_dihedral_angle_4_deg21.17
r_dihedral_angle_3_deg16.018
r_dihedral_angle_1_deg6.508
r_scangle_it2.556
r_scbond_it1.594
r_angle_refined_deg1.408
r_mcangle_it0.973
r_mcbond_it0.566
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.862
r_dihedral_angle_4_deg21.17
r_dihedral_angle_3_deg16.018
r_dihedral_angle_1_deg6.508
r_scangle_it2.556
r_scbond_it1.594
r_angle_refined_deg1.408
r_mcangle_it0.973
r_mcbond_it0.566
r_nbtor_refined0.304
r_nbd_refined0.202
r_symmetry_vdw_refined0.194
r_xyhbond_nbd_refined0.138
r_chiral_restr0.091
r_symmetry_hbond_refined0.082
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9838
Nucleic Acid Atoms
Solvent Atoms241
Heterogen Atoms52

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CHESSdata collection
HKL-2000data reduction