X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZBQPDB ENTRY 1ZBQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.6289MymaA.01582.a.A1 PS00686 at 57.1 mg/mL against JCSG+ screen condition C11, 0.1 M NaOAc pH 4.6, 2 M ammonium sulfate with 25% ethylene glycol as cryo-protectant, crystal tracking ID 217306c11, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3246.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.52α = 90
b = 129.9β = 109.86
c = 91.86γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.97946ALS5.0.1

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
11.85099.80.05218.14.6166151165849-3
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)
11.81.8599.80.4353.354.3

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 1ZBQ1.850157404833499.840.161640.159930.19405RANDOM27.037
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]
0.590.48-0.50.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.61
r_dihedral_angle_4_deg16.174
r_dihedral_angle_3_deg11.689
r_dihedral_angle_1_deg5.647
r_scangle_it3.475
r_scbond_it2.174
r_angle_refined_deg1.365
r_mcangle_it1.276
r_mcbond_it0.743
r_chiral_restr0.108
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.61
r_dihedral_angle_4_deg16.174
r_dihedral_angle_3_deg11.689
r_dihedral_angle_1_deg5.647
r_scangle_it3.475
r_scbond_it2.174
r_angle_refined_deg1.365
r_mcangle_it1.276
r_mcbond_it0.743
r_chiral_restr0.108
r_bond_refined_d0.014
r_gen_planes_refined0.007
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12121
Nucleic Acid Atoms
Solvent Atoms1273
Heterogen Atoms45

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction