X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QEW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429825% PEG 3350, 0.1M HEPES, pH 7.4, 10mM MnCl2, 10mM GTP, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1943.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.713α = 90
b = 118.851β = 108.84
c = 60.704γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++blue osmic confocal2007-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.54

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
11.910089.30.11710.56.7421284212822
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)
11.91.9746.10.5753.82168

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 REPLACEMENTTHROUGHOUT2QEW1.932.624210242102213489.160.1950.1950.1930.229RANDOM18.023
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]
0.540.29-0.390.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.108
r_dihedral_angle_4_deg14.458
r_dihedral_angle_3_deg13.963
r_dihedral_angle_1_deg5.126
r_angle_refined_deg1.01
r_scangle_it0.911
r_scbond_it0.572
r_mcangle_it0.399
r_nbtor_refined0.299
r_mcbond_it0.217
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.108
r_dihedral_angle_4_deg14.458
r_dihedral_angle_3_deg13.963
r_dihedral_angle_1_deg5.126
r_angle_refined_deg1.01
r_scangle_it0.911
r_scbond_it0.572
r_mcangle_it0.399
r_nbtor_refined0.299
r_mcbond_it0.217
r_nbd_refined0.172
r_symmetry_vdw_refined0.148
r_symmetry_hbond_refined0.107
r_xyhbond_nbd_refined0.105
r_metal_ion_refined0.093
r_chiral_restr0.068
r_bond_refined_d0.006
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4801
Nucleic Acid Atoms
Solvent Atoms495
Heterogen Atoms40

Software

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