X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZYJPDB entry 1ZYJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293100 mM MES, 20-30% PEG4000, 50 mM n-BOG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2745.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.77α = 90
b = 74.12β = 93.72
c = 71.6γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plateOsmic2009-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54170

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
12.2540990.04619.772.653525034895-334.109
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)
2.252.3599.30.254.52.564281

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1ZYJ2.2529.953525034893873990.190.1880.26RANDOM28.201
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]
0.84-0.42-0.43-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.981
r_dihedral_angle_3_deg17.95
r_dihedral_angle_4_deg15.03
r_dihedral_angle_1_deg6.488
r_scangle_it3.311
r_scbond_it2.195
r_angle_refined_deg1.613
r_mcangle_it1.597
r_mcbond_it0.926
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.981
r_dihedral_angle_3_deg17.95
r_dihedral_angle_4_deg15.03
r_dihedral_angle_1_deg6.488
r_scangle_it3.311
r_scbond_it2.195
r_angle_refined_deg1.613
r_mcangle_it1.597
r_mcbond_it0.926
r_nbtor_refined0.309
r_nbd_refined0.211
r_symmetry_vdw_refined0.198
r_xyhbond_nbd_refined0.178
r_symmetry_hbond_refined0.144
r_chiral_restr0.102
r_bond_refined_d0.016
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5451
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms152

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling