X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E1QPDB ENTRY 1E1Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.32775.5% PEG 6000, 10% glycerol, 4% methanol, 0.05M sodium acetate, 0.5mM nickel sulphate, 0.5mM AMP/PNP, 0.025 mM ADP, 2mM magnesium chloride, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7555.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.524α = 90
b = 294.132β = 101.67
c = 190.432γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2003-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 5ID-B1.0APS5ID-B

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
12.630940.07411.73.6346124
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)
12.62.7940.4062.6236073

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)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 1E1Q2.8202293909286907593899.940.207310.206590.24412RANDOM70.39
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]
1.52-0.91-0.42-1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.257
r_dihedral_angle_4_deg18.689
r_dihedral_angle_3_deg16.083
r_scangle_it6.462
r_dihedral_angle_1_deg5.626
r_scbond_it4.401
r_mcangle_it2.828
r_mcbond_it1.645
r_angle_refined_deg1.346
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.257
r_dihedral_angle_4_deg18.689
r_dihedral_angle_3_deg16.083
r_scangle_it6.462
r_dihedral_angle_1_deg5.626
r_scbond_it4.401
r_mcangle_it2.828
r_mcbond_it1.645
r_angle_refined_deg1.346
r_nbtor_refined0.307
r_symmetry_hbond_refined0.276
r_symmetry_vdw_refined0.237
r_nbd_refined0.216
r_metal_ion_refined0.139
r_xyhbond_nbd_refined0.137
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms72173
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms485

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing