X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UPKPDB ENTRY 1UPK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.515 % PEG 20000, 0.1 M MES PH 6.5, 4.4 % GAMMA BUTYROLACTONE
Crystal Properties
Matthews coefficientSolvent content
238

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.625α = 90
b = 94.012β = 90
c = 96.327γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC Q4 CCD2003-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.63098.60.11816.35.320073
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)
12.62.6990.60.5222.74.3

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 DIFFRACTIONMADTHROUGHOUTPDB ENTRY 1UPK2.6251949652498.60.2140.2120.28RANDOM18.9
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]
-2.294.08-1.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.908
r_dihedral_angle_1_deg5.882
r_scangle_it2.29
r_mcangle_it2.161
r_scbond_it2.034
r_angle_refined_deg1.647
r_mcbond_it1.197
r_symmetry_hbond_refined0.475
r_symmetry_vdw_refined0.301
r_nbd_refined0.293
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.908
r_dihedral_angle_1_deg5.882
r_scangle_it2.29
r_mcangle_it2.161
r_scbond_it2.034
r_angle_refined_deg1.647
r_mcbond_it1.197
r_symmetry_hbond_refined0.475
r_symmetry_vdw_refined0.301
r_nbd_refined0.293
r_xyhbond_nbd_refined0.179
r_chiral_restr0.118
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5107
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing