X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2X8YPDB ENTRY 2X8Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5pH 7.5
Crystal Properties
Matthews coefficientSolvent content
4.2270.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 172.707α = 90
b = 172.707β = 90
c = 101.696γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2010-01-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.965097.90.0612.72.381351225.7
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)
11.962.0390.30.194.72.2

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 2X8Y1.9632.6475613397997.870.195090.194030.21461RANDOM32.74
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]
-0.04-0.02-0.040.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.843
r_dihedral_angle_4_deg15.233
r_dihedral_angle_3_deg12.647
r_dihedral_angle_1_deg4.818
r_scangle_it1.807
r_scbond_it1.054
r_angle_refined_deg1.009
r_mcangle_it0.684
r_mcbond_it0.348
r_chiral_restr0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.843
r_dihedral_angle_4_deg15.233
r_dihedral_angle_3_deg12.647
r_dihedral_angle_1_deg4.818
r_scangle_it1.807
r_scbond_it1.054
r_angle_refined_deg1.009
r_mcangle_it0.684
r_mcbond_it0.348
r_chiral_restr0.079
r_bond_refined_d0.007
r_gen_planes_refined0.004
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4873
Nucleic Acid Atoms
Solvent Atoms490
Heterogen Atoms153

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing