X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E3ZPDB ENTRY 2E3Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82980.1M Tris, 20-22%(w/v) PEG 3350, 0.23M MgCl2, 12.5mM sodium formate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0640.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.83α = 90
b = 103.511β = 105.37
c = 94.802γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2009-03-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0000Photon FactoryBL-5A

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
11.633096.90.08820.95.62174002107661
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)
1.631.6995.30.5034.55.621633

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 2E3Z1.6329.91928061015594.450.167040.164410.21771RANDOM14.638
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]
0.02-0.23-0.30.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.267
r_dihedral_angle_4_deg16.729
r_dihedral_angle_3_deg11.491
r_dihedral_angle_1_deg4.705
r_sphericity_free3.986
r_scangle_it3.512
r_scbond_it2.469
r_sphericity_bonded2.45
r_mcangle_it1.553
r_rigid_bond_restr1.452
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.267
r_dihedral_angle_4_deg16.729
r_dihedral_angle_3_deg11.491
r_dihedral_angle_1_deg4.705
r_sphericity_free3.986
r_scangle_it3.512
r_scbond_it2.469
r_sphericity_bonded2.45
r_mcangle_it1.553
r_rigid_bond_restr1.452
r_angle_refined_deg1.439
r_mcbond_it1.018
r_chiral_restr0.107
r_gen_planes_refined0.008
r_bond_refined_d0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14791
Nucleic Acid Atoms
Solvent Atoms3100
Heterogen Atoms32

Software

Software
Software NamePurpose
HKL-2000data collection
CNSrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing