X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AZ9Published hexagonal structure without Mn or solvent atoms

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.3277Tris, PEG 4k, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
4.471.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.42α = 90
b = 177.42β = 90
c = 96.42γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATERIGAKU RAXIS IICYALE MIRRORS1997-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.99324.465584-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9763.45.69

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPublished hexagonal structure without Mn or solvent atoms1.938.3563537199193.060.152430.152430.151850.17047RANDOM17.996
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]
0.250.120.25-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.877
r_dihedral_angle_4_deg15.035
r_dihedral_angle_3_deg11.876
r_dihedral_angle_1_deg6.042
r_scangle_it4.006
r_mcangle_it2.815
r_scbond_it2.635
r_mcbond_it2.481
r_angle_refined_deg1.28
r_angle_other_deg0.829
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.877
r_dihedral_angle_4_deg15.035
r_dihedral_angle_3_deg11.876
r_dihedral_angle_1_deg6.042
r_scangle_it4.006
r_mcangle_it2.815
r_scbond_it2.635
r_mcbond_it2.481
r_angle_refined_deg1.28
r_angle_other_deg0.829
r_mcbond_other0.595
r_symmetry_vdw_other0.286
r_symmetry_hbond_refined0.211
r_nbd_refined0.205
r_symmetry_vdw_refined0.205
r_nbd_other0.182
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.151
r_nbtor_other0.082
r_chiral_restr0.077
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3500
Nucleic Acid Atoms
Solvent Atoms607
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling