X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H9GPDB entry 3H9G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5291.224-26% Pentaerythritol ethoxylate (15/4 EO/OH, Hampton Research), 50 mM Na Hepes pH 7.5, 100 mM MgSO4, 9 mM AMPCPP, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
Crystal Properties
Matthews coefficientSolvent content
1.9336.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.841α = 90
b = 138.004β = 92.21
c = 80.816γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plateRosenbaum-Rock vertical focusing mirror2007-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.97926APS22-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
12.35098.90.08117.144.1546115461141.7
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)
12.32.3891.10.3643.35027

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 3H9G2.339.975421553753271599.160.2030.1990.1960.255RANDOM44.194
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]
0.73-0.08-1.570.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.605
r_dihedral_angle_4_deg19.488
r_dihedral_angle_3_deg16.999
r_dihedral_angle_1_deg5.873
r_scangle_it1.972
r_angle_refined_deg1.248
r_scbond_it1.229
r_mcangle_it0.912
r_mcbond_it0.511
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.605
r_dihedral_angle_4_deg19.488
r_dihedral_angle_3_deg16.999
r_dihedral_angle_1_deg5.873
r_scangle_it1.972
r_angle_refined_deg1.248
r_scbond_it1.229
r_mcangle_it0.912
r_mcbond_it0.511
r_nbtor_refined0.303
r_symmetry_vdw_refined0.205
r_nbd_refined0.198
r_xyhbond_nbd_refined0.162
r_symmetry_hbond_refined0.141
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10482
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms142

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
X-GENdata scaling
HKL-2000data reduction
REFMACphasing