X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IU8PDB ENTRY 2IU8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5PROTEIN WAS CRYSTALLIZED FROM 1.2M AMMONIUM SULFATE, 0.1M MES, PH 6.5, 2% PEG 400, AND 1MM DTT.
Crystal Properties
Matthews coefficientSolvent content
2.9958.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.679α = 90
b = 98.679β = 90
c = 284.505γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103IMAGE PLATERIGAKU-MSC R-AXIS-4++OSMIC MIRRORS2004-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
12.74096.50.1111.34.738280
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)
12.72.7890.40.5123.3

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 2IU82.793.2536293191096.30.2120.2090.273RANDOM41.55
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]
1.061.06-2.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.775
r_dihedral_angle_3_deg19.112
r_dihedral_angle_4_deg17.659
r_dihedral_angle_1_deg6.508
r_scangle_it1.958
r_angle_refined_deg1.387
r_scbond_it1.187
r_mcangle_it1.029
r_mcbond_it0.578
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.775
r_dihedral_angle_3_deg19.112
r_dihedral_angle_4_deg17.659
r_dihedral_angle_1_deg6.508
r_scangle_it1.958
r_angle_refined_deg1.387
r_scbond_it1.187
r_mcangle_it1.029
r_mcbond_it0.578
r_nbtor_refined0.308
r_nbd_refined0.219
r_symmetry_hbond_refined0.214
r_symmetry_vdw_refined0.185
r_xyhbond_nbd_refined0.174
r_chiral_restr0.091
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7911
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling