X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GJO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4293100 mM PCTP buffer, pH 4, supplemented with 25% PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.0640.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.35α = 90
b = 183.272β = 112.33
c = 42.387γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-09-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.345.82990.0510.0560.022.86.852463
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.4397.30.5040.5010.2080.812.83

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 REPLACEMENTTHROUGHOUT3GJO2.345.8225149132499.490.232370.230390.27059RANDOM58.427
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]
0.72-0.21-2.251.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.052
r_dihedral_angle_4_deg18.697
r_dihedral_angle_3_deg15.531
r_dihedral_angle_1_deg4.399
r_long_range_B_refined3.053
r_long_range_B_other2.983
r_angle_refined_deg1.165
r_mcangle_it1.128
r_mcangle_other1.127
r_angle_other_deg0.924
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.052
r_dihedral_angle_4_deg18.697
r_dihedral_angle_3_deg15.531
r_dihedral_angle_1_deg4.399
r_long_range_B_refined3.053
r_long_range_B_other2.983
r_angle_refined_deg1.165
r_mcangle_it1.128
r_mcangle_other1.127
r_angle_other_deg0.924
r_scangle_other0.896
r_mcbond_it0.629
r_mcbond_other0.629
r_scbond_it0.497
r_scbond_other0.497
r_chiral_restr0.064
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms4333
Nucleic Acid Atoms
Solvent Atoms114
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing