X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4Q5PPDB ENTRY 4Q5P

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829128% w/v PEG, 0.3 M ammonium phosphate, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.1160.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.96α = 90
b = 105.96β = 90
c = 149.95γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702013-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6A1.0781NSLSX6A

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
12.10319.5299.50.09539.3929.125279251551.368.48
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.1032.2298.20.5498.4829.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 4Q5P2.10319.522515523843131199.740.184840.18270.22318RANDOM30.737
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]
-2.19-2.194.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.801
r_dihedral_angle_3_deg18.866
r_dihedral_angle_4_deg11.118
r_dihedral_angle_1_deg6.47
r_mcangle_it4.73
r_mcbond_it3.545
r_mcbond_other3.528
r_scbond_it3.45
r_angle_refined_deg1.979
r_angle_other_deg1.242
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.801
r_dihedral_angle_3_deg18.866
r_dihedral_angle_4_deg11.118
r_dihedral_angle_1_deg6.47
r_mcangle_it4.73
r_mcbond_it3.545
r_mcbond_other3.528
r_scbond_it3.45
r_angle_refined_deg1.979
r_angle_other_deg1.242
r_chiral_restr0.136
r_bond_refined_d0.021
r_gen_planes_other0.018
r_gen_planes_refined0.013
r_bond_other_d0.007
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_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms2460
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms129

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
Blu-Icedata collection