X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M54PDB entry 1M54

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.529823% PEG 3350, 0.2 Li2SO4, 100 mM BIS-TRIS 6.5, vapor diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.141.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.914α = 90
b = 138.157β = 90
c = 75.192γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDK-B pair of biomorph mirrors for vertical and horizontal focusing2009-10-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0332APS23-ID-D

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
11.85095.90.0812.484482142962
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)
1.81.8672.20.4035.83209

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1M541.841.264482141020218695.660.16120.15950.1932RANDOM20.0323
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.118
r_dihedral_angle_4_deg20.164
r_dihedral_angle_3_deg13.642
r_dihedral_angle_1_deg5.585
r_scangle_it3.864
r_scbond_it2.341
r_mcangle_it1.55
r_angle_refined_deg1.348
r_mcbond_it0.842
r_angle_other_deg0.706
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.118
r_dihedral_angle_4_deg20.164
r_dihedral_angle_3_deg13.642
r_dihedral_angle_1_deg5.585
r_scangle_it3.864
r_scbond_it2.341
r_mcangle_it1.55
r_angle_refined_deg1.348
r_mcbond_it0.842
r_angle_other_deg0.706
r_mcbond_other0.219
r_chiral_restr0.084
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3826
Nucleic Acid Atoms
Solvent Atoms435
Heterogen Atoms58

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
BALBESphasing