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
2.3547.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.35α = 90
b = 93.872β = 90
c = 108.547γ = 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 Mirror2008-08-29MSINGLE 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
11.523099.40.03350.37.15822957879129
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)
11.521.5798.40.3095.46.75755

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 1EZF1.5223.757805293399.410.166030.164410.19569RANDOM26.56
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]
1.95-1.54-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.201
r_dihedral_angle_3_deg13.999
r_dihedral_angle_4_deg13.771
r_scangle_it5.873
r_dihedral_angle_1_deg4.724
r_scbond_it3.88
r_mcangle_it2.374
r_rigid_bond_restr1.768
r_mcbond_it1.435
r_angle_refined_deg1.404
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.201
r_dihedral_angle_3_deg13.999
r_dihedral_angle_4_deg13.771
r_scangle_it5.873
r_dihedral_angle_1_deg4.724
r_scbond_it3.88
r_mcangle_it2.374
r_rigid_bond_restr1.768
r_mcbond_it1.435
r_angle_refined_deg1.404
r_chiral_restr0.091
r_gen_planes_refined0.008
r_bond_refined_d0.007
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 Atoms335
Heterogen Atoms

Software

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