X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2A8DPDB ENTRY 2A8D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52950.1 M HEPES, 1.8 M ammonium sulfate, 4% PEG 400, 100 mM sodium bicarbonate, 12 mg/mL protein, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.7555.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 229.593α = 90
b = 144.437β = 94.43
c = 104.891γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F20.980CHESSF2

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
12122.16989.60.0550.05519.14.8205440
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)
122.1155.60.4750.4751.93.118560

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 2A8D229.752054022054021034789.590.2030.2030.2010.236RANDOM36.165
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]
-0.060.040.040.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.853
r_dihedral_angle_4_deg17.163
r_dihedral_angle_3_deg15.298
r_dihedral_angle_1_deg5.542
r_scangle_it2.307
r_scbond_it1.598
r_angle_refined_deg1.192
r_mcangle_it0.941
r_angle_other_deg0.856
r_mcbond_it0.782
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.853
r_dihedral_angle_4_deg17.163
r_dihedral_angle_3_deg15.298
r_dihedral_angle_1_deg5.542
r_scangle_it2.307
r_scbond_it1.598
r_angle_refined_deg1.192
r_mcangle_it0.941
r_angle_other_deg0.856
r_mcbond_it0.782
r_symmetry_vdw_other0.248
r_nbd_refined0.213
r_symmetry_hbond_refined0.205
r_nbd_other0.189
r_symmetry_vdw_refined0.185
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.149
r_mcbond_other0.134
r_nbtor_other0.087
r_xyhbond_nbd_other0.083
r_chiral_restr0.071
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20197
Nucleic Acid Atoms
Solvent Atoms604
Heterogen Atoms121

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction