X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GG3pdb id 3GG3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.1521-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8
Crystal Properties
Matthews coefficientSolvent content
3.3763.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.45α = 90
b = 99.45β = 90
c = 100.51γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2011-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54178

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
12.2533.51000.08511.94.11760044.5
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)
12.252.371000.6442.14

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 id 3GG32.2530.971670489299.960.208190.20670.23651RANDOM47.21
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]
-0.07-0.04-0.070.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.864
r_dihedral_angle_4_deg18.255
r_dihedral_angle_3_deg13.369
r_dihedral_angle_1_deg5.702
r_long_range_B_refined5.652
r_long_range_B_other5.65
r_scangle_other3.253
r_mcangle_it2.575
r_mcangle_other2.574
r_scbond_it1.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.864
r_dihedral_angle_4_deg18.255
r_dihedral_angle_3_deg13.369
r_dihedral_angle_1_deg5.702
r_long_range_B_refined5.652
r_long_range_B_other5.65
r_scangle_other3.253
r_mcangle_it2.575
r_mcangle_other2.574
r_scbond_it1.92
r_scbond_other1.92
r_mcbond_it1.544
r_mcbond_other1.519
r_angle_refined_deg1.485
r_angle_other_deg1.337
r_chiral_restr0.083
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.007
r_gen_planes_other0.007
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1778
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing