X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z62PDB ENTRY 2Z62, 2Z64
experimental modelPDB 2Z64PDB ENTRY 2Z62, 2Z64

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.52960.2M Ammonium Sulfate, 0.1M Sodium Acetate, 20% PEG 4000, 5% Ethanol, pH 4.5, VAPOR DIFFUSION, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
3.0960.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.192α = 90
b = 80.987β = 93.01
c = 107.762γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2007-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.75090.40.08933086027898

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 2Z62, 2Z642.72027898146292.350.24030.237630.28874RANDOM50.542
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]
2.91-1.93-2.26-0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.442
r_dihedral_angle_3_deg18.508
r_dihedral_angle_4_deg17.737
r_scangle_it9.905
r_scbond_it6.769
r_dihedral_angle_1_deg6.584
r_mcangle_it4.228
r_mcbond_it2.658
r_angle_refined_deg1.393
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.442
r_dihedral_angle_3_deg18.508
r_dihedral_angle_4_deg17.737
r_scangle_it9.905
r_scbond_it6.769
r_dihedral_angle_1_deg6.584
r_mcangle_it4.228
r_mcbond_it2.658
r_angle_refined_deg1.393
r_nbtor_refined0.319
r_symmetry_vdw_refined0.26
r_nbd_refined0.232
r_xyhbond_nbd_refined0.172
r_symmetry_hbond_refined0.16
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6646
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms287

Software

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