X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ZE5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529316% PEG 8K, 3% MPD, 0.1 M imidazole buffer pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.4148.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.59α = 90
b = 97.47β = 97.66
c = 105.27γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.98ESRFBM14

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
11.43598.70.07410.75.3398539
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)
11.41.4297.30.54235.3

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 REPLACEMENTTHROUGHOUT4ZE51.422.373735251977198.70.1320.130.158RANDOM14.27
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]
-0.530.040.65-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.845
r_dihedral_angle_4_deg17.452
r_dihedral_angle_3_deg11.86
r_dihedral_angle_1_deg7.25
r_long_range_B_refined7.202
r_long_range_B_other7.201
r_scangle_other4.363
r_scbond_it2.976
r_scbond_other2.976
r_angle_refined_deg2.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.845
r_dihedral_angle_4_deg17.452
r_dihedral_angle_3_deg11.86
r_dihedral_angle_1_deg7.25
r_long_range_B_refined7.202
r_long_range_B_other7.201
r_scangle_other4.363
r_scbond_it2.976
r_scbond_other2.976
r_angle_refined_deg2.67
r_mcangle_other2.573
r_mcangle_it2.572
r_mcbond_it1.726
r_mcbond_other1.718
r_angle_other_deg1.081
r_chiral_restr0.159
r_bond_refined_d0.029
r_gen_planes_refined0.015
r_bond_other_d0.002
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15140
Nucleic Acid Atoms
Solvent Atoms2578
Heterogen Atoms173

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing