X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZE3PDB entry 2ZE3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4289JCSG+c2: 20% PEG6000, 1M LiCl, 0.1M NaCit pH4.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4750.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 218.6α = 90
b = 91.18β = 91.53
c = 110.01γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002013-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.9798APS21-ID-F

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
11.75099.80.05517.153.7623688523635414.8
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)
11.71.7499.90.4393.513.7817451

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 2ZE31.746.292245121184399.770.159110.157520.18912RANDOM21.112
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]
-0.610.66-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.964
r_dihedral_angle_4_deg18.159
r_dihedral_angle_3_deg11.925
r_long_range_B_refined6.042
r_long_range_B_other6.042
r_dihedral_angle_1_deg5.466
r_scangle_other3.319
r_scbond_it2.115
r_scbond_other2.114
r_mcangle_it2.064
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.964
r_dihedral_angle_4_deg18.159
r_dihedral_angle_3_deg11.925
r_long_range_B_refined6.042
r_long_range_B_other6.042
r_dihedral_angle_1_deg5.466
r_scangle_other3.319
r_scbond_it2.115
r_scbond_other2.114
r_mcangle_it2.064
r_mcangle_other2.064
r_angle_refined_deg1.621
r_mcbond_it1.317
r_mcbond_other1.317
r_angle_other_deg0.855
r_chiral_restr0.096
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.001
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 Atoms14455
Nucleic Acid Atoms
Solvent Atoms1797
Heterogen Atoms41

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling