X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EZFPDB ENTRY 1EZF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529820% PEG 2000 MME, 0.01M NiCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0840.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.776α = 90
b = 76.657β = 90
c = 82.501γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210Vertically Collimating Premirror, Toroidal Focusing Mirror2008-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.00000NSRRCBL13B1

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
11.523099.50.04540.985141351144127.4
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)
11.521.5799.30.5094.18.15077

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 1EZF1.5224.751082259899.490.162840.160170.21376RANDOM25.876
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]
-0.890.98-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.606
r_dihedral_angle_4_deg17.621
r_dihedral_angle_3_deg13.123
r_scangle_it5.268
r_dihedral_angle_1_deg4.883
r_scbond_it3.547
r_mcangle_it2.137
r_rigid_bond_restr1.644
r_angle_refined_deg1.419
r_mcbond_it1.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.606
r_dihedral_angle_4_deg17.621
r_dihedral_angle_3_deg13.123
r_scangle_it5.268
r_dihedral_angle_1_deg4.883
r_scbond_it3.547
r_mcangle_it2.137
r_rigid_bond_restr1.644
r_angle_refined_deg1.419
r_mcbond_it1.312
r_chiral_restr0.09
r_bond_refined_d0.007
r_gen_planes_refined0.007
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
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2705
Nucleic Acid Atoms
Solvent Atoms459
Heterogen Atoms2

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling