X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J3IPDB entry 1J3I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629517% 2-Methyl-2,4-Pentanediol, 10% PEG 4000, 0.1M Potassium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.4449.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.681α = 90
b = 137.25β = 90
c = 189.27γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9998APS19-BM

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
12.45099.50.0618.2453964581811
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)
12.42.4995.80.244372

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTPDB entry 1J3I2.443.154539643565215895.160.2080.2060.241RANDOM37.46
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]
-3.065.28-2.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.667
r_dihedral_angle_4_deg16.647
r_dihedral_angle_3_deg16.332
r_dihedral_angle_1_deg5.24
r_scangle_it1.379
r_angle_refined_deg1.113
r_scbond_it0.833
r_mcangle_it0.756
r_mcbond_it0.429
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.667
r_dihedral_angle_4_deg16.647
r_dihedral_angle_3_deg16.332
r_dihedral_angle_1_deg5.24
r_scangle_it1.379
r_angle_refined_deg1.113
r_scbond_it0.833
r_mcangle_it0.756
r_mcbond_it0.429
r_nbtor_refined0.301
r_nbd_refined0.186
r_symmetry_vdw_refined0.159
r_xyhbond_nbd_refined0.119
r_symmetry_hbond_refined0.103
r_chiral_restr0.067
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8028
Nucleic Acid Atoms
Solvent Atoms307
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
CCP4phasing
DENZOdata reduction