X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y79PDB 1Y79

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52890.2M MgCl2, 0.1M sodium cacodylate, 20% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.58α = 97.72
b = 66.94β = 90.71
c = 102γ = 117.37
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.7533890.0990.9825.61.9128529
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)
11.751.7855.20.2772.31.8

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 1Y791.7533122085643689.180.186510.185090.21326RANDOM16.319
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]
-0.43-0.160.030.30.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.484
r_dihedral_angle_4_deg13.747
r_dihedral_angle_3_deg12.537
r_dihedral_angle_1_deg7.06
r_long_range_B_refined4.307
r_long_range_B_other4.025
r_scangle_other2.314
r_mcangle_it1.584
r_mcangle_other1.584
r_angle_refined_deg1.445
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.484
r_dihedral_angle_4_deg13.747
r_dihedral_angle_3_deg12.537
r_dihedral_angle_1_deg7.06
r_long_range_B_refined4.307
r_long_range_B_other4.025
r_scangle_other2.314
r_mcangle_it1.584
r_mcangle_other1.584
r_angle_refined_deg1.445
r_scbond_it1.423
r_scbond_other1.423
r_angle_other_deg0.983
r_mcbond_it0.971
r_mcbond_other0.971
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10510
Nucleic Acid Atoms
Solvent Atoms1026
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing