X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MZ2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.05 M HEPES pH 7.5, 0.05 M NaCl, 7-13% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.1943.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.022α = 90
b = 111.022β = 90
c = 396.361γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2004-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I7111.087MAX III711

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
12.619.9696.90.1784.29.375003
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)
12.62.6975.80.956

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 REPLACEMENTTHROUGHOUT5MZ22.619.9670943382296.90.1750.1710.238RANDOM28.76
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]
0.020.02-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.655
r_dihedral_angle_4_deg16.063
r_dihedral_angle_3_deg14.304
r_dihedral_angle_1_deg7.482
r_long_range_B_refined2.228
r_long_range_B_other2.22
r_angle_refined_deg1.556
r_mcangle_it1.16
r_mcangle_other1.16
r_angle_other_deg1.015
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.655
r_dihedral_angle_4_deg16.063
r_dihedral_angle_3_deg14.304
r_dihedral_angle_1_deg7.482
r_long_range_B_refined2.228
r_long_range_B_other2.22
r_angle_refined_deg1.556
r_mcangle_it1.16
r_mcangle_other1.16
r_angle_other_deg1.015
r_scangle_other0.923
r_mcbond_it0.65
r_mcbond_other0.65
r_scbond_it0.507
r_scbond_other0.507
r_chiral_restr0.098
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19532
Nucleic Acid Atoms
Solvent Atoms353
Heterogen Atoms160

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing