X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W4XPDB ENTRY 1W4X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529522% PEG4000, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2545.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.007α = 90
b = 139.983β = 98.38
c = 67.569γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2010-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-ID

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
12.04569.99299.50.1179.53.767586
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)
12.0452.1298.60.5663.46635

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 1W4X2.04548.34167485341698.830.19210.18950.2403RANDOM26.14
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]
0.97-0.370.26-1.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.469
r_dihedral_angle_4_deg16.271
r_dihedral_angle_3_deg15.21
r_dihedral_angle_1_deg5.863
r_scangle_it2.897
r_scbond_it1.811
r_mcangle_it1.224
r_angle_refined_deg1.216
r_mcbond_it0.712
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.469
r_dihedral_angle_4_deg16.271
r_dihedral_angle_3_deg15.21
r_dihedral_angle_1_deg5.863
r_scangle_it2.897
r_scbond_it1.811
r_mcangle_it1.224
r_angle_refined_deg1.216
r_mcbond_it0.712
r_nbtor_refined0.306
r_nbd_refined0.197
r_symmetry_vdw_refined0.176
r_xyhbond_nbd_refined0.148
r_symmetry_hbond_refined0.137
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8516
Nucleic Acid Atoms
Solvent Atoms593
Heterogen Atoms106

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
MOLREPphasing