X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DRGPDB ENTRY 4DRG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.6200MM NA MALONATE PH=4.6, 20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.1542.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.206α = 90
b = 65.655β = 95.98
c = 85.156γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 1SOLEILPROXIMA 1

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
1242.3599.20.089.63.5236492
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)
122.0599.80.452.93.5

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 4DRG253.7522328131598.850.190560.188050.23176RANDOM25.963
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]
0.19-0.120.82-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.999
r_dihedral_angle_4_deg18.687
r_dihedral_angle_3_deg13.776
r_dihedral_angle_1_deg5.758
r_mcangle_it2.599
r_scbond_it2.396
r_angle_refined_deg1.823
r_mcbond_it1.648
r_mcbond_other1.648
r_angle_other_deg1.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.999
r_dihedral_angle_4_deg18.687
r_dihedral_angle_3_deg13.776
r_dihedral_angle_1_deg5.758
r_mcangle_it2.599
r_scbond_it2.396
r_angle_refined_deg1.823
r_mcbond_it1.648
r_mcbond_other1.648
r_angle_other_deg1.312
r_chiral_restr0.102
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.004
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 Atoms2342
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms132

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing