X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WVASeMet-labelled HcgF PDB ENTRY 3WVA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529820%(w/v)PEG3000, 200mM sodium chloride, 100mM HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9135.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.31α = 90
b = 73.11β = 102.22
c = 45.53γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2011-09-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.270SLSX10SA

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
11.75098.60.02339.883.6231585-321.029
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.896.80.0420.0525.62

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 REPLACEMENTTHROUGHOUTSeMet-labelled HcgF PDB ENTRY 3WVA1.744.2831563160098.810.14760.14520.1908RANDOM14.677
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]
0.01-0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.798
r_dihedral_angle_4_deg24.353
r_dihedral_angle_3_deg14.922
r_dihedral_angle_1_deg5.936
r_scbond_it2.363
r_angle_refined_deg2.286
r_mcangle_it1.357
r_mcbond_it0.926
r_chiral_restr0.19
r_bond_refined_d0.022
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.798
r_dihedral_angle_4_deg24.353
r_dihedral_angle_3_deg14.922
r_dihedral_angle_1_deg5.936
r_scbond_it2.363
r_angle_refined_deg2.286
r_mcangle_it1.357
r_mcbond_it0.926
r_chiral_restr0.19
r_bond_refined_d0.022
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2668
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
MOLREPphasing