X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KPR1KPR, 1B6E
experimental modelPDB 1B6E1KPR, 1B6E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82911.8M ammonium sulfate, 0.3-0.7% sucrose, 100 mM Tris (8.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
5.9579.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 345.983α = 90
b = 345.983β = 90
c = 345.983γ = 90
Symmetry
Space GroupI 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103CCDADSC QUANTUM 3152006-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.2ALS8.2.2

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
14.41701000.1666.934.422619
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)
14.44.561000.4891.0326.32189

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1KPR, 1B6E4.4167.882260021445115599.950.320540.35529RANDOM97.161
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
r_dihedral_angle_2_deg36.601
r_dihedral_angle_3_deg18.979
r_dihedral_angle_4_deg13.292
r_dihedral_angle_1_deg6.202
r_angle_refined_deg1.088
r_angle_other_deg0.84
r_symmetry_vdw_other0.257
r_scangle_it0.251
r_nbd_refined0.209
r_symmetry_vdw_refined0.206
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.601
r_dihedral_angle_3_deg18.979
r_dihedral_angle_4_deg13.292
r_dihedral_angle_1_deg6.202
r_angle_refined_deg1.088
r_angle_other_deg0.84
r_symmetry_vdw_other0.257
r_scangle_it0.251
r_nbd_refined0.209
r_symmetry_vdw_refined0.206
r_nbd_other0.205
r_nbtor_refined0.182
r_scbond_it0.168
r_xyhbond_nbd_refined0.162
r_mcangle_it0.126
r_mcbond_it0.089
r_nbtor_other0.082
r_chiral_restr0.066
r_mcbond_other0.029
r_xyhbond_nbd_other0.028
r_symmetry_hbond_refined0.028
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10146
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing