X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KPRPDB ENTRY 1KPR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529825% PEG 3350, 50mM diammonium tartrate, 5mM Thioflavin T, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1743.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.349α = 90
b = 28.467β = 91.42
c = 74.983γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-11-14MSINGLE WAVELENGTH
21x-ray
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E1.00APS24-ID-E
2SYNCHROTRONNSLS BEAMLINE X251.00NSLSX25

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
1,21.65098.30.0820.0828.891.938793
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.61.8388.3

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1KPR1.629.272065326034139899.80.1910.1890.223RANDOM31.14
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]
0.070.05-0.04-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.171
r_dihedral_angle_4_deg17.169
r_dihedral_angle_3_deg13.336
r_dihedral_angle_1_deg6.641
r_scangle_it3.174
r_mcangle_it2.889
r_scbond_it2.077
r_mcbond_it1.775
r_angle_refined_deg1.542
r_angle_other_deg1.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.171
r_dihedral_angle_4_deg17.169
r_dihedral_angle_3_deg13.336
r_dihedral_angle_1_deg6.641
r_scangle_it3.174
r_mcangle_it2.889
r_scbond_it2.077
r_mcbond_it1.775
r_angle_refined_deg1.542
r_angle_other_deg1.12
r_mcbond_other0.538
r_chiral_restr0.093
r_bond_refined_d0.012
r_gen_planes_other0.012
r_gen_planes_refined0.009
r_bond_other_d0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1628
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms83

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling