X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UQYPDB ENTRY 3UQY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.929812% PEG4000, 0.1M NaCl, 0.1M NaAc, 0.2M NH4Ac, 0.001M DTT, 0.02% DDM, Tris/HCl, 0.0003M NQNO (a menaquinone analog), pH 5.9, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.448.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126α = 90
b = 165.3β = 90
c = 212.8γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97908ESRFID29

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
13.249.1297.80.0811.3573321138472-389.561
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)
13.23.397.11.0541.16

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3UQY3.3256749166832329899.270.20180.20180.19990.236RANDOM105.957
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]
7.45-6.89-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.949
r_dihedral_angle_3_deg17.099
r_dihedral_angle_4_deg15.385
r_dihedral_angle_1_deg5.28
r_scangle_it3.834
r_scbond_it2.306
r_mcangle_it1.661
r_angle_refined_deg1.161
r_mcbond_it0.837
r_chiral_restr0.082
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.949
r_dihedral_angle_3_deg17.099
r_dihedral_angle_4_deg15.385
r_dihedral_angle_1_deg5.28
r_scangle_it3.834
r_scbond_it2.306
r_mcangle_it1.661
r_angle_refined_deg1.161
r_mcbond_it0.837
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms30002
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms316

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction