X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J3HPDB ENTRY 2J3H

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.9 M NA CITRATE, 0.1 M MES PH 6.5, 0.1 M MGSO4, 10 % GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
3.1661.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 170.93α = 90
b = 177.09β = 90
c = 181.66γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-07-02MSINGLE 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
12.0973.0699.20.0520.14.9318966239
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)
12.092.1599.10.662.44.9

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 2J3H2.173.0643164911598999.0950.2240.22270.2428RANDOM41.087
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]
0.838-0.754-0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.933
r_dihedral_angle_4_deg19.741
r_dihedral_angle_3_deg14.589
r_scbond_it6.397
r_scangle_it5.47
r_dihedral_angle_1_deg5.292
r_mcangle_it3.652
r_mcbond_it2.298
r_angle_other_deg1.608
r_angle_refined_deg1.362
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.933
r_dihedral_angle_4_deg19.741
r_dihedral_angle_3_deg14.589
r_scbond_it6.397
r_scangle_it5.47
r_dihedral_angle_1_deg5.292
r_mcangle_it3.652
r_mcbond_it2.298
r_angle_other_deg1.608
r_angle_refined_deg1.362
r_mcbond_other0.538
r_nbd_other0.368
r_nbd_refined0.215
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.12
r_chiral_restr0.087
r_xyhbond_nbd_other0.07
r_bond_refined_d0.009
r_bond_other_d0.008
r_gen_planes_refined0.006
r_gen_planes_other0.006
r_nbtor_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_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 Atoms29081
Nucleic Acid Atoms
Solvent Atoms976
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing