X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KSIPDB ENTRY 1KSI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.2293HANGING DROP VAPOR DIFFUSION AT 293K. RESERVOIR WAS 20% PEG 3350, 0.28M KI. DROPS WERE 2 MICROL OF PSAO AT 21.58MG/ML IN 0.1M KPO4 PH 7.2, PLUS 1 MICROL OF 0.1M KPO4 PH 7.5, PLUS 1 MICROL OF RESERVOIR SOLUTION. THE CRYSTAL WAS CRYOPROTECTED BY SOAKING FOR 5 MIN IN 5 MICROL OF 0.2M KI, 25% PEG 3350 AND 15% GLYCEROL UNDER 30MICROL OF PARAFFIN IN A SITTING DROP DEPRESSION. THE CRYSTAL WAS EXPOSED TO XENON GAS FOR 5 MINUTES, INITIALLY AT PRESSURE OF 100 PSI THEN INCREASING TO A FINAL PRESSURE OF 220 PSI, USING A XENON CHAMBER (HAMPTON RESEARCH). AFTER THE XENON WAS RELEASED FROM THE CHAMBER, THE CRYSTAL WAS SNAP-FROZEN IN LIQUID NITROGEN WITHIN 1-3 S.
Crystal Properties
Matthews coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.507α = 90
b = 196.268β = 107.46
c = 89.665γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOSMIC MIRROR2004-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
12.2429.8299.80.07174.75141039-328.5
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)
12.242.398.90.177.74.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1KSI2.2429.88133957708299.80.1810.1790.224RANDOM19.5
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]
-0.52-1.020.06-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.218
r_scangle_it5.974
r_scbond_it4.158
r_mcangle_it2.698
r_mcbond_it1.539
r_angle_refined_deg1.322
r_angle_other_deg0.806
r_nbd_other0.236
r_symmetry_vdw_other0.222
r_symmetry_vdw_refined0.202
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.218
r_scangle_it5.974
r_scbond_it4.158
r_mcangle_it2.698
r_mcbond_it1.539
r_angle_refined_deg1.322
r_angle_other_deg0.806
r_nbd_other0.236
r_symmetry_vdw_other0.222
r_symmetry_vdw_refined0.202
r_nbd_refined0.188
r_symmetry_hbond_refined0.177
r_xyhbond_nbd_refined0.149
r_chiral_restr0.083
r_nbtor_other0.082
r_bond_refined_d0.012
r_metal_ion_refined0.011
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_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 Atoms20648
Nucleic Acid Atoms
Solvent Atoms585
Heterogen Atoms304

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing