X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NNOPDB ENTRY 2NNO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52910.1M sodium citrate pH5.5, 0.1M sodium acetate pH4.5 and 26% of PEG4000 , VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.243.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.27α = 90
b = 57.386β = 90
c = 159.552γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100FLAT PANELMAR555 flatpanel detector2011-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.815EMBL/DESY, HAMBURGX11

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
11.9540.1781000.1350.13597.3386143861421.6
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)
11.952.061000.4860.4861.57.45561

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 2NNO1.9540.1783465438534388099.950.1750.1750.1690.235RANDOM19.689
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]
0.030.78-0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.37
r_dihedral_angle_4_deg16.64
r_dihedral_angle_3_deg14.271
r_dihedral_angle_1_deg7.021
r_scangle_it4.129
r_scbond_it2.966
r_angle_refined_deg2.026
r_mcangle_it1.91
r_mcbond_it1.187
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.37
r_dihedral_angle_4_deg16.64
r_dihedral_angle_3_deg14.271
r_dihedral_angle_1_deg7.021
r_scangle_it4.129
r_scbond_it2.966
r_angle_refined_deg2.026
r_mcangle_it1.91
r_mcbond_it1.187
r_nbtor_refined0.31
r_symmetry_vdw_refined0.226
r_nbd_refined0.206
r_symmetry_hbond_refined0.174
r_xyhbond_nbd_refined0.163
r_metal_ion_refined0.162
r_chiral_restr0.143
r_bond_refined_d0.024
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4135
Nucleic Acid Atoms
Solvent Atoms553
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection
MOLREPphasing