X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QRRPDB ENTRY 1QRR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293ammonium sulfate, sodium chloride, MES buffer, NAD+, UDP-glucose, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.565

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 159.682α = 90
b = 159.682β = 90
c = 99.038γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray105IMAGE PLATERIGAKU RAXIS IV++Osmic Max-Flux confocal, multilayer mirrors2000-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.63098.80.09413.54.4282759-315.24
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)
11.61.6697.60.3621.52.1

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1QRR1.6308270482704412598.80.1770.185R-free flags were assigned using the CCP4 suite, based on a standard set of flags used for all SQD1 structural refinements.17.7
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]
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.09
c_angle_deg1.29
c_scangle_it1.012
c_improper_angle_d0.76
c_mcangle_it0.69
c_scbond_it0.661
c_mcbond_it0.409
c_bond_d0.0053
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.09
c_angle_deg1.29
c_scangle_it1.012
c_improper_angle_d0.76
c_mcangle_it0.69
c_scbond_it0.661
c_mcbond_it0.409
c_bond_d0.0053
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3033
Nucleic Acid Atoms
Solvent Atoms398
Heterogen Atoms90

Software

Software
Software NamePurpose
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
CCP4data reduction
CNSrefinement
CrystalCleardata reduction
CCP4data scaling
CNSphasing