X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2G15PDB entry 2G15

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5298The protein in 20mM Tris-HCl pH 8.0, 0.5M NaCl, 5% glycerol, 2mM BME, 2.5 mM AMP-PNP, 10 mM MgCl2, 5mM peptide (ADEPNYETWG) was mixed with crystallization buffer (15% PEG 8000, 0.2M ammonium sulfate, and 0.1 M Sodium cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.2344.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.47α = 90
b = 90.057β = 102.44
c = 69.253γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2007-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.42599.80.06721.63.52454424544-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.42.4999.70.2935.23.42456

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 2G152.424.7923326123299.540.207610.204140.27392RANDOM39.11
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]
5.72-0.91-3.14-2.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.742
r_dihedral_angle_4_deg16.83
r_dihedral_angle_3_deg15.862
r_dihedral_angle_1_deg5.194
r_scangle_it2.174
r_scbond_it1.618
r_mcangle_it1.316
r_angle_refined_deg1.201
r_mcbond_it0.766
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.742
r_dihedral_angle_4_deg16.83
r_dihedral_angle_3_deg15.862
r_dihedral_angle_1_deg5.194
r_scangle_it2.174
r_scbond_it1.618
r_mcangle_it1.316
r_angle_refined_deg1.201
r_mcbond_it0.766
r_nbtor_refined0.299
r_nbd_refined0.195
r_symmetry_vdw_refined0.181
r_symmetry_hbond_refined0.168
r_metal_ion_refined0.16
r_xyhbond_nbd_refined0.135
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3934
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms69

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing