X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1I9YPDB ENTRY 1I9Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP529320% PEG 6000, 0.1M citric acid pH 5, 2mM biphenyl 2,3',4,5',6-pentakisphosphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1643.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.796α = 90
b = 61.177β = 91.9
c = 114.32γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-225mirrors2010-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.844.7799.60.1520.1527.94.6154001533859.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.9599.50.720.7224.62227

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 1I9Y2.820146211452475599.340.216440.216440.213580.27247RANDOM35.337
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]
-0.682.19-0.381.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.215
r_dihedral_angle_4_deg18.752
r_dihedral_angle_3_deg16.575
r_dihedral_angle_1_deg6.288
r_scangle_it1.201
r_angle_refined_deg1.146
r_angle_other_deg0.807
r_scbond_it0.702
r_mcangle_it0.471
r_mcbond_it0.245
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.215
r_dihedral_angle_4_deg18.752
r_dihedral_angle_3_deg16.575
r_dihedral_angle_1_deg6.288
r_scangle_it1.201
r_angle_refined_deg1.146
r_angle_other_deg0.807
r_scbond_it0.702
r_mcangle_it0.471
r_mcbond_it0.245
r_chiral_restr0.065
r_mcbond_other0.046
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4784
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms1

Software

Software
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling