X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 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
2.4850.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.721α = 90
b = 95.499β = 90
c = 163.574γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDADSC QUANTUM 4r2005-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.97944NSLSX4A

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
12.15091.80.05513.23.477387
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)
12.12.1860.10.2741.64996

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 IPG42.1147.3576279385892.620.180.1780.221RANDOM23.615
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]
-0.16-0.070.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.697
r_dihedral_angle_4_deg17.78
r_dihedral_angle_3_deg13.19
r_dihedral_angle_1_deg5.826
r_scangle_it2.19
r_scbond_it1.357
r_angle_refined_deg1.138
r_mcangle_it0.824
r_mcbond_it0.517
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.697
r_dihedral_angle_4_deg17.78
r_dihedral_angle_3_deg13.19
r_dihedral_angle_1_deg5.826
r_scangle_it2.19
r_scbond_it1.357
r_angle_refined_deg1.138
r_mcangle_it0.824
r_mcbond_it0.517
r_nbtor_refined0.301
r_symmetry_hbond_refined0.297
r_symmetry_vdw_refined0.211
r_nbd_refined0.19
r_xyhbond_nbd_refined0.129
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9843
Nucleic Acid Atoms
Solvent Atoms626
Heterogen Atoms52

Software

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