X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DM1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529830% PEG 400, 0.2M CaCl2 0.1M Na Hepes 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9837.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.057α = 90
b = 39.068β = 137.03
c = 37.832γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.97625APS23-ID-B

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
11.84048154818

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 REPLACEMENTTHROUGHOUT3DM11.827.18466021996.740.2240.2220.274RANDOM11.545
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]
0.971.78-1.22.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.944
r_dihedral_angle_4_deg13.996
r_dihedral_angle_3_deg11.622
r_dihedral_angle_1_deg6.397
r_scangle_it3.111
r_scbond_it2.314
r_angle_refined_deg1.623
r_mcangle_it1.346
r_mcbond_it0.962
r_symmetry_hbond_refined0.393
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.944
r_dihedral_angle_4_deg13.996
r_dihedral_angle_3_deg11.622
r_dihedral_angle_1_deg6.397
r_scangle_it3.111
r_scbond_it2.314
r_angle_refined_deg1.623
r_mcangle_it1.346
r_mcbond_it0.962
r_symmetry_hbond_refined0.393
r_symmetry_vdw_refined0.36
r_nbtor_refined0.311
r_xyhbond_nbd_refined0.23
r_nbd_refined0.223
r_chiral_restr0.106
r_bond_refined_d0.019
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms393
Nucleic Acid Atoms
Solvent Atoms28
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction