X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3O4HPDB ENTRY 3O4H

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529378 mM sodium acetate buffer, 2.2% w/v PEG Mw4000, 5.2 mM dithiothreitol, 0.34 mM EDTA. Protein crystals were soaked in the inhibitor solution., pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4850.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.58α = 105.15
b = 97.3β = 103.96
c = 99.16γ = 100.26
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210Sagitally focusing Ge(220) and a multilayer2011-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9334ESRFID14-1

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
12.552086.40.07113.382.186828168281-3
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)
12.552.6251.10.5052.16

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 3O4H2.5519.856483364833344186.520.213980.211520.25963RANDOM, IMPORTED FROM ISOSTRUCTURAL DATA SET OF PDB ENTRY 3O4H.33.726
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]
-0.140.420.110.630.14-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.251
r_dihedral_angle_4_deg17.548
r_dihedral_angle_3_deg15.06
r_dihedral_angle_1_deg5.844
r_long_range_B_refined5.192
r_long_range_B_other5.151
r_scangle_other3.458
r_mcangle_it3.012
r_mcangle_other2.969
r_scbond_it2.226
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.251
r_dihedral_angle_4_deg17.548
r_dihedral_angle_3_deg15.06
r_dihedral_angle_1_deg5.844
r_long_range_B_refined5.192
r_long_range_B_other5.151
r_scangle_other3.458
r_mcangle_it3.012
r_mcangle_other2.969
r_scbond_it2.226
r_scbond_other2.184
r_mcbond_it1.881
r_mcbond_other1.881
r_angle_refined_deg1.47
r_angle_other_deg1.294
r_chiral_restr0.076
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.007
r_gen_planes_other0.006
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17267
Nucleic Acid Atoms
Solvent Atoms674
Heterogen Atoms49

Software

Software
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling