X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52982% PEG 400, 2M K2HPO4/NaH2PO4, 0.5mM zaragozic acid A, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5551.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.873α = 90
b = 153.153β = 91.72
c = 91.855γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rVertically Collimating Premirror, Toroidal Focusing Mirror2009-07-24MSINGLE 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
11.893099.40.0620.83.7189042187887131.4
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)
11.891.9699.20.4722.33.618909

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 1EZF1.8927.7187819943199.370.150350.147870.19717RANDOM38.25
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]
-1.261.36-0.391.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.251
r_dihedral_angle_4_deg17.109
r_dihedral_angle_3_deg14.552
r_scangle_it5.026
r_dihedral_angle_1_deg4.884
r_scbond_it3.345
r_mcangle_it2.083
r_rigid_bond_restr1.723
r_angle_refined_deg1.4
r_mcbond_it1.246
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.251
r_dihedral_angle_4_deg17.109
r_dihedral_angle_3_deg14.552
r_scangle_it5.026
r_dihedral_angle_1_deg4.884
r_scbond_it3.345
r_mcangle_it2.083
r_rigid_bond_restr1.723
r_angle_refined_deg1.4
r_mcbond_it1.246
r_chiral_restr0.095
r_bond_refined_d0.007
r_gen_planes_refined0.006
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 Atoms16139
Nucleic Acid Atoms
Solvent Atoms1390
Heterogen Atoms326

Software

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