X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z2C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.8291.153M Sodium Chloride, 0.1M Sodium Acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Crystal Properties
Matthews coefficientSolvent content
2.6854.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.435α = 90
b = 59.435β = 90
c = 138.09γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.1554.5931000.1220.1226.111.814207142053.83.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.271001000.5830.5831.311.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUT1z2c2.1554.553.8142051415271099.920.162290.1590.226RANDOM19.992
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]
0.080.08-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.976
r_dihedral_angle_4_deg22.198
r_dihedral_angle_3_deg15.283
r_dihedral_angle_1_deg6.034
r_scangle_it4.424
r_scbond_it2.957
r_mcangle_it1.891
r_angle_refined_deg1.733
r_mcbond_it1.183
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.976
r_dihedral_angle_4_deg22.198
r_dihedral_angle_3_deg15.283
r_dihedral_angle_1_deg6.034
r_scangle_it4.424
r_scbond_it2.957
r_mcangle_it1.891
r_angle_refined_deg1.733
r_mcbond_it1.183
r_nbtor_refined0.302
r_symmetry_vdw_refined0.29
r_nbd_refined0.206
r_xyhbond_nbd_refined0.172
r_chiral_restr0.125
r_symmetry_hbond_refined0.12
r_bond_refined_d0.016
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1420
Nucleic Acid Atoms
Solvent Atoms157
Heterogen Atoms43

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata reduction
CCP4data scaling