X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R29 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.529875 mM NaAcetate, 900 mM K2HPO4, 700 NaH2PO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.8768.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.55α = 90
b = 150.55β = 90
c = 312.25γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152004-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.979APS19-ID

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
12.648.7970.072012.36505063099
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)
2.62.7298.50.545.312.3

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1R292.648.76505063035306997.060.2210.2190.26RANDOM71.704
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]
-1.62-0.81-1.622.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.1
r_dihedral_angle_4_deg22.138
r_dihedral_angle_3_deg20.349
r_dihedral_angle_1_deg7.098
r_scangle_it4.703
r_scbond_it2.858
r_mcangle_it2.275
r_angle_refined_deg1.783
r_mcbond_it1.629
r_nbtor_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.1
r_dihedral_angle_4_deg22.138
r_dihedral_angle_3_deg20.349
r_dihedral_angle_1_deg7.098
r_scangle_it4.703
r_scbond_it2.858
r_mcangle_it2.275
r_angle_refined_deg1.783
r_mcbond_it1.629
r_nbtor_refined0.32
r_symmetry_vdw_refined0.307
r_nbd_refined0.25
r_symmetry_hbond_refined0.249
r_xyhbond_nbd_refined0.167
r_chiral_restr0.119
r_bond_refined_d0.018
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8950
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection