X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DHIPDB ENTRY 2DHI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROPVAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
1.8934.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.747α = 90
b = 48.449β = 92.2
c = 64.323γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102010-01-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

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
1110097.10.05446.86.3102125
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)
111.0295.30.298.55.8

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 2DHI114.4596954510497.080.106060.105050.12563RANDOM7.642
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]
-0.020.010.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.642
r_dihedral_angle_4_deg17.897
r_dihedral_angle_3_deg13.127
r_dihedral_angle_1_deg7.09
r_scangle_it5.549
r_scbond_it3.937
r_mcangle_it2.77
r_angle_refined_deg1.944
r_mcbond_it1.799
r_rigid_bond_restr1.486
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.642
r_dihedral_angle_4_deg17.897
r_dihedral_angle_3_deg13.127
r_dihedral_angle_1_deg7.09
r_scangle_it5.549
r_scbond_it3.937
r_mcangle_it2.77
r_angle_refined_deg1.944
r_mcbond_it1.799
r_rigid_bond_restr1.486
r_angle_other_deg1.012
r_mcbond_other0.539
r_chiral_restr0.126
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_gen_planes_other0.003
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1824
Nucleic Acid Atoms
Solvent Atoms308
Heterogen Atoms23

Software

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