X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EK9pdb entry 1EK9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42910.6% detergent mixture of n-dodecyl-beta-D glucopyranoside, n-hexyl-beta-D glucopyranoside, n-heptyl-beta-D glucopyranoside and n-octyl-beta-D glucopyranoside, 1.5% 1,2,3-heptanetriol, 7% polyethylene glycol 2000 monomethyl ether, 10% polyethylene glycol 400, 10mM NaCl, 20mM MgCl2, 20mM Tris, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
4.6973.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 265.276α = 90
b = 265.276β = 90
c = 96.253γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.11.488SRSPX14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.753095.60.0955.11.8655996273012
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)
2.752.8294.40.3132.11.863790

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1EK92.7530.43216559959556317495.630.265790.26570.263760.30473RANDOM47.736
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_1_deg6.609
r_scangle_it4.05
r_scbond_it2.449
r_angle_refined_deg1.874
r_mcangle_it1.339
r_mcbond_it0.598
r_symmetry_vdw_refined0.537
r_symmetry_hbond_refined0.533
r_nbd_refined0.238
r_xyhbond_nbd_refined0.215
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.609
r_scangle_it4.05
r_scbond_it2.449
r_angle_refined_deg1.874
r_mcangle_it1.339
r_mcbond_it0.598
r_symmetry_vdw_refined0.537
r_symmetry_hbond_refined0.533
r_nbd_refined0.238
r_xyhbond_nbd_refined0.215
r_chiral_restr0.137
r_bond_refined_d0.018
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9915
Nucleic Acid Atoms
Solvent Atoms305
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing