X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YC6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277CONDITIONS AROUND 0.1M BIS-TRIS(PH6.5), 0.2M SODIUM NITRATE 20% PEG3350, PROTEIN AT 10-12 MG/ML, 0.5Mm INHIBITOR
Crystal Properties
Matthews coefficientSolvent content
2.7655.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.704α = 90
b = 97.232β = 90
c = 108.564γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.987DiamondI24

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
12.3372.4399.80.0510.81.921580
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)
12.332.4197.70.422.41.9

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 REPLACEMENTTHROUGHOUT4YC62.3372.4320503107799.780.203170.200920.24586RANDOM47.498
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]
1.9-1.73-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.208
r_dihedral_angle_4_deg20.6
r_dihedral_angle_3_deg18.415
r_long_range_B_other9.98
r_long_range_B_refined9.975
r_dihedral_angle_1_deg7.635
r_scangle_other7.605
r_mcangle_it6.103
r_mcangle_other6.101
r_scbond_it4.905
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.208
r_dihedral_angle_4_deg20.6
r_dihedral_angle_3_deg18.415
r_long_range_B_other9.98
r_long_range_B_refined9.975
r_dihedral_angle_1_deg7.635
r_scangle_other7.605
r_mcangle_it6.103
r_mcangle_other6.101
r_scbond_it4.905
r_scbond_other4.905
r_mcbond_other4.049
r_mcbond_it4.048
r_angle_other_deg3.598
r_angle_refined_deg1.85
r_chiral_restr0.117
r_bond_refined_d0.016
r_gen_planes_other0.009
r_gen_planes_refined0.008
r_bond_other_d
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 Atoms2943
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing