X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2UBP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.3WELL SOLUTIONS: 1.9 M AMMONIUM SULPHATE, 4MM PHENYLPHOSPHORODIAMIDATE, 1OOMM SODIUM CITRATE PH 6.3. PROTEIN SOLUTION: 20 C, 3 MICROLITERS PROTEIN SOLUTION ( 11 MG/ML IN 20 MM TRIS HCL PH 8.0 + 4MM PHENYLPHOSPHORODIAMIDATE) + 3 MICROLITERS PRECIPITANT SOLUTION, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.532α = 90
b = 131.532β = 90
c = 188.451γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHBENT MIRROR1997-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7AEMBL/DESY, HAMBURGBW7A

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
122099.90.150.159.7213.3865301-3
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)
122.0499.90.5360.5362.87.56

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTRFREE2UBP21865301130699.90.1580.1580.2RANDOM15.87
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]
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor30.5
p_staggered_tor15
p_planar_tor5.9
p_scangle_it4.634
p_scbond_it3.855
p_mcangle_it2.077
p_mcbond_it1.648
p_multtor_nbd0.25
p_singtor_nbd0.183
p_planar_d0.033
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor30.5
p_staggered_tor15
p_planar_tor5.9
p_scangle_it4.634
p_scbond_it3.855
p_mcangle_it2.077
p_mcbond_it1.648
p_multtor_nbd0.25
p_singtor_nbd0.183
p_planar_d0.033
p_angle_d0.028
p_bond_d0.009
p_angle_deg
p_hb_or_metal_coord
p_plane_restr
p_chiral_restr
p_xhyhbond_nbd
p_xyhbond_nbd
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6055
Nucleic Acid Atoms
Solvent Atoms841
Heterogen Atoms7

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling