X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZPBPDB ENTRY 2ZPB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529320% PEG 8000, 0.1M Tris-HCl pH7.5, 300mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4650.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.976α = 90
b = 60.002β = 125.08
c = 81.707γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 3152006-05-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.00000Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.4866.81598.37387713.7

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 2ZPB1.48869876370598.940.166690.165290.19332RANDOM15.955
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.975
r_dihedral_angle_4_deg17.815
r_dihedral_angle_3_deg10.875
r_dihedral_angle_1_deg5.247
r_scangle_it2.318
r_scbond_it1.506
r_angle_refined_deg1.186
r_mcangle_it0.971
r_mcbond_it0.626
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.975
r_dihedral_angle_4_deg17.815
r_dihedral_angle_3_deg10.875
r_dihedral_angle_1_deg5.247
r_scangle_it2.318
r_scbond_it1.506
r_angle_refined_deg1.186
r_mcangle_it0.971
r_mcbond_it0.626
r_nbtor_refined0.308
r_nbd_refined0.225
r_symmetry_hbond_refined0.164
r_symmetry_vdw_refined0.149
r_xyhbond_nbd_refined0.125
r_chiral_restr0.077
r_metal_ion_refined0.038
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3295
Nucleic Acid Atoms
Solvent Atoms690
Heterogen Atoms15

Software

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