X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DGGPDB entry 3DGG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529385% of 0.2M Ammonium sulfate, 30% w/v PEG 4000 in 15% water - with 10 microliters of 1M NaOH per 1ml crystallization solution, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4750.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.206α = 101.5
b = 70.602β = 102.94
c = 87.849γ = 98.32
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.9537ESRFBM14

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
12.43097.70.10310.83.435860-1.5
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)
2.42.4996.70.6491.43.13531

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 3DGG2.43033630177497.720.222040.218560.28632RANDOM44.74
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]
-4.980.96-0.873.552.082.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.836
r_dihedral_angle_3_deg15.749
r_dihedral_angle_4_deg12.843
r_scangle_it6.367
r_dihedral_angle_1_deg5.318
r_scbond_it4.805
r_mcangle_it4.053
r_mcbond_it3.142
r_angle_refined_deg1.026
r_mcbond_other0.895
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.836
r_dihedral_angle_3_deg15.749
r_dihedral_angle_4_deg12.843
r_scangle_it6.367
r_dihedral_angle_1_deg5.318
r_scbond_it4.805
r_mcangle_it4.053
r_mcbond_it3.142
r_angle_refined_deg1.026
r_mcbond_other0.895
r_angle_other_deg0.826
r_symmetry_vdw_other0.25
r_symmetry_hbond_refined0.202
r_nbd_other0.198
r_symmetry_vdw_refined0.177
r_nbtor_refined0.176
r_nbd_refined0.163
r_xyhbond_nbd_refined0.127
r_nbtor_other0.081
r_chiral_restr0.061
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6543
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing