X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4PXNModel identified with SIMBAD, MR done with 4pxnA as per MoRDa

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5290Molecular Dimensions Morpheus screen, H2: 10% PEG 8000, 20% EG: 20mM of each amino acid: sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine: 100mM MES / Imidazole pH 6.5: BuceA.00020.r.B1.PW37259 at 20mg/ml + 2.5mM NAD: cryo: direct: tray 299802h2: puck bit3-4
Crystal Properties
Matthews coefficientSolvent content
2.7352.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.67α = 90
b = 124.98β = 90
c = 246.2γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002018-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
12.145.81399.80.0820.0920.99712.784.8989932929.36
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.151000.5070.5660.8633.085.062

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTModel identified with SIMBAD, MR done with 4pxnA as per MoRDa2.145.8131.3499314204099.840.14790.14710.189334.8319
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11238
Nucleic Acid Atoms
Solvent Atoms1198
Heterogen Atoms360

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
SIMBADphasing
MoRDaphasing
Cootmodel building