X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GE7PDB ENTRY 2GE7 4 copies

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.629830% PEG 4000, 100 mM Tris-HCl pH 8.6, 800 mM LiCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4349.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.99α = 90
b = 128.534β = 90
c = 71.435γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray178CCDADSC QUANTUM 4Bent conical Si-mirror (Rh coated). Bent Ge(111) monochromator2003-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9000APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12129.47395.80.1150.1154.84.4695046625822
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.1197.30.0130.012760.53.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 2GE7 4 copies2.247.782695045117926151000.240.240.2370.291RANDOM32.178
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]
-0.020.08-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.144
r_dihedral_angle_3_deg19.133
r_dihedral_angle_4_deg19.002
r_dihedral_angle_1_deg8.373
r_scangle_it4.531
r_scbond_it2.906
r_angle_refined_deg1.919
r_mcangle_it1.719
r_mcbond_it1.066
r_symmetry_hbond_refined0.473
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.144
r_dihedral_angle_3_deg19.133
r_dihedral_angle_4_deg19.002
r_dihedral_angle_1_deg8.373
r_scangle_it4.531
r_scbond_it2.906
r_angle_refined_deg1.919
r_mcangle_it1.719
r_mcbond_it1.066
r_symmetry_hbond_refined0.473
r_nbtor_refined0.322
r_symmetry_vdw_refined0.285
r_nbd_refined0.251
r_xyhbond_nbd_refined0.18
r_chiral_restr0.142
r_bond_refined_d0.02
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6881
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
CCP4data scaling
PHASERphasing
CNSphasing