X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PENPDB entry 2PEN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52931.5-2.5 M Sodium acetate, 0.1 M HEPES-NaOH pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.9475.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.446α = 90
b = 93.446β = 90
c = 411.544γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-08-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.00000ESRFID29

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
13.4103.14299.60.0890.0893.43.426126
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)
13.43.5899.80.5030.5031.53.63742

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 2PEN3.42025915131999.280.2550.2530.294RANDOM106.428
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]
-1.79-1.793.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.851
r_dihedral_angle_3_deg23.28
r_dihedral_angle_4_deg21.608
r_dihedral_angle_1_deg5.837
r_scangle_it2.404
r_angle_refined_deg1.319
r_scbond_it1.295
r_mcangle_it1.012
r_mcbond_it0.54
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.851
r_dihedral_angle_3_deg23.28
r_dihedral_angle_4_deg21.608
r_dihedral_angle_1_deg5.837
r_scangle_it2.404
r_angle_refined_deg1.319
r_scbond_it1.295
r_mcangle_it1.012
r_mcbond_it0.54
r_nbtor_refined0.307
r_nbd_refined0.256
r_symmetry_vdw_refined0.198
r_xyhbond_nbd_refined0.14
r_symmetry_hbond_refined0.121
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4727
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
MOLREPphasing