X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M6KPDB entry 1M6K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529810% (v/v) PEG 8000, 50 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0539.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.041α = 90
b = 71.613β = 99.18
c = 93.139γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2008-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.1APS21-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
11.43096.60.07413.55.186546
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)
11.41.4588.10.2932.97834

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 1M6K1.428.2986509432696.450.1850.1840.206RANDOM15.268
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]
0.120.25-0.570.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.853
r_dihedral_angle_4_deg14.722
r_dihedral_angle_3_deg11.882
r_dihedral_angle_1_deg5.571
r_scangle_it3.102
r_scbond_it1.885
r_angle_refined_deg1.365
r_mcangle_it1.23
r_mcbond_it0.664
r_nbtor_refined0.333
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.853
r_dihedral_angle_4_deg14.722
r_dihedral_angle_3_deg11.882
r_dihedral_angle_1_deg5.571
r_scangle_it3.102
r_scbond_it1.885
r_angle_refined_deg1.365
r_mcangle_it1.23
r_mcbond_it0.664
r_nbtor_refined0.333
r_nbd_refined0.227
r_symmetry_vdw_refined0.186
r_symmetry_hbond_refined0.17
r_xyhbond_nbd_refined0.127
r_chiral_restr0.079
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3905
Nucleic Acid Atoms
Solvent Atoms434
Heterogen Atoms62

Software

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