X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XWDPDB ENTRY 1XWD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1M HEPES PH 7.5, 10% (V/V) ISOPROPANOL AND 20% (W/V) POLYETHYLENE GLYCOL 4000
Crystal Properties
Matthews coefficientSolvent content
2.8857.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.716α = 60.3
b = 95.478β = 80.02
c = 95.675γ = 75.35
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCH MX-300MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-DAPS21-ID-D

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
12.55097.40.0715.86.470869
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)
12.52.695.80.43.35.1

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 1XWD2.547.96727035991000.236830.235080.26901RANDOM61.853
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]
3.13-2.36-1.13-1.292.14-2.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.075
r_dihedral_angle_3_deg19.929
r_dihedral_angle_4_deg18.673
r_dihedral_angle_1_deg7.495
r_scangle_it3.173
r_mcangle_it2.013
r_scbond_it1.927
r_angle_refined_deg1.267
r_mcbond_it1.103
r_angle_other_deg0.669
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.075
r_dihedral_angle_3_deg19.929
r_dihedral_angle_4_deg18.673
r_dihedral_angle_1_deg7.495
r_scangle_it3.173
r_mcangle_it2.013
r_scbond_it1.927
r_angle_refined_deg1.267
r_mcbond_it1.103
r_angle_other_deg0.669
r_mcbond_other0.079
r_chiral_restr0.074
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.001
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_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 Atoms11911
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms210

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
XSCALEdata scaling
PHASERphasing