X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GKFPDB entry 3GKF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52984% PEG 400, 100 mM MgCl2, 2.3 M Ammonium Sulfate, pH 7.5, vapor diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.346.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.352α = 89.51
b = 105.451β = 79.79
c = 173.415γ = 90.34
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42008-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X26C1.00NSLSX26C

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
12.555.7381.70.0657.52.132717015448445.3
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)
12.52.6467.80.2791.81.718764

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTPDB entry 3GKF2.555.73127454127454633867.420.2060.2060.2050.235RANDOM35.975
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]
-2.42-1.47-0.471.712.80.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.896
r_dihedral_angle_4_deg15.075
r_dihedral_angle_3_deg14.675
r_scangle_it6.004
r_dihedral_angle_1_deg5.579
r_scbond_it3.239
r_mcangle_it1.802
r_angle_refined_deg1.358
r_mcbond_it0.837
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.896
r_dihedral_angle_4_deg15.075
r_dihedral_angle_3_deg14.675
r_scangle_it6.004
r_dihedral_angle_1_deg5.579
r_scbond_it3.239
r_mcangle_it1.802
r_angle_refined_deg1.358
r_mcbond_it0.837
r_chiral_restr0.09
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms42260
Nucleic Acid Atoms
Solvent Atoms334
Heterogen Atoms280

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection