X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H5APDB entry 3H5A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8291.224-26% Pentaerythritol ethoxylate (15/4 EO/OH, Hampton Research), 50 mM Tris-HCl pH 8.0, 50 mM (NH4)2SO4, 10 mM MccA-N7isoAsn, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
Crystal Properties
Matthews coefficientSolvent content
1.9436.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.929α = 90
b = 138.217β = 92.38
c = 80.799γ = 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
12.25096.70.06521.9144.1607986079833.6
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)
12.22.2890.50.3713.65645

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 3H5A2.246.886212460091304196.730.2060.2030.2030.261RANDOM36.297
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]
0.44-0.03-1.050.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.142
r_dihedral_angle_4_deg17.641
r_dihedral_angle_3_deg15.297
r_dihedral_angle_1_deg5.28
r_scangle_it2.217
r_scbond_it1.591
r_mcangle_it1.116
r_angle_refined_deg1.103
r_mcbond_it0.794
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.142
r_dihedral_angle_4_deg17.641
r_dihedral_angle_3_deg15.297
r_dihedral_angle_1_deg5.28
r_scangle_it2.217
r_scbond_it1.591
r_mcangle_it1.116
r_angle_refined_deg1.103
r_mcbond_it0.794
r_nbtor_refined0.303
r_nbd_refined0.201
r_symmetry_vdw_refined0.195
r_xyhbond_nbd_refined0.146
r_symmetry_hbond_refined0.131
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10767
Nucleic Acid Atoms
Solvent Atoms511
Heterogen Atoms39

Software

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