X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GBJPDB ENTRY 2GBJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.9293.1527-32% PEG 6000, 4-12% Acetone, 50 mM Sodium Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
1.8935

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.046α = 79.91
b = 45.895β = 74.99
c = 54.382γ = 81.33
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002004-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

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
11.995.890.70.0849.62.731801216333
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)
11.992.0689.889.80.1574.22.661603

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2GBJ1.995.8180121633185090.730.246380.246380.244030.28668RANDOM18.166
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]
0.951.32-1.08-1.480.290.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.735
r_dihedral_angle_4_deg12.801
r_dihedral_angle_3_deg12.476
r_dihedral_angle_1_deg5.022
r_angle_refined_deg0.857
r_angle_other_deg0.743
r_scangle_it0.733
r_scbond_it0.479
r_mcangle_it0.263
r_mcbond_it0.233
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.735
r_dihedral_angle_4_deg12.801
r_dihedral_angle_3_deg12.476
r_dihedral_angle_1_deg5.022
r_angle_refined_deg0.857
r_angle_other_deg0.743
r_scangle_it0.733
r_scbond_it0.479
r_mcangle_it0.263
r_mcbond_it0.233
r_nbd_other0.163
r_nbd_refined0.157
r_symmetry_vdw_other0.152
r_nbtor_refined0.151
r_symmetry_hbond_refined0.139
r_symmetry_vdw_refined0.118
r_xyhbond_nbd_refined0.086
r_nbtor_other0.075
r_chiral_restr0.05
r_mcbond_other0.034
r_bond_refined_d0.005
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2597
Nucleic Acid Atoms
Solvent Atoms254
Heterogen Atoms

Software

Software
Software NamePurpose
d*TREKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
JDirectordata collection