X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z7XPDB Entry 1Z7X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82930.1 M Tris pH 8.0, 0.02 M MgCl2, 25 % (w/v) PAA 5100, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9658.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.69α = 90
b = 84.69β = 90
c = 130.47γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHBENT MIRRORS2008-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0000SLSX06SA

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
11.6529.899.80.03851.619.83395433885-3
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)
11.651.71000.3769.7117.82844

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB Entry 1Z7X1.6529.83388533885169599.790.136910.136910.134480.18253RANDOM31.347
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]
-0.35-0.18-0.350.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.621
r_sphericity_free36.296
r_sphericity_bonded24.158
r_dihedral_angle_3_deg15.781
r_dihedral_angle_4_deg13.71
r_rigid_bond_restr8.228
r_dihedral_angle_1_deg4.973
r_angle_refined_deg2.271
r_chiral_restr0.16
r_bond_refined_d0.023
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.621
r_sphericity_free36.296
r_sphericity_bonded24.158
r_dihedral_angle_3_deg15.781
r_dihedral_angle_4_deg13.71
r_rigid_bond_restr8.228
r_dihedral_angle_1_deg4.973
r_angle_refined_deg2.271
r_chiral_restr0.16
r_bond_refined_d0.023
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1543
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms6

Software

Software
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling