5ICE

Crystal structure of (S)-norcoclaurine 6-O-methyltransferase with S-adenosyl-L-homocysteine and norlaudanosoline


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5293Peg3350, Sodium Chloride, Phosphate Citrate buffer
Crystal Properties
Matthews coefficientSolvent content
2.0941.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.72α = 90
b = 109.13β = 90
c = 40.95γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.9798ESRFBM30A

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
11.696.70.04626.96.243013-320.495
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)
11.61.783.50.2494.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.643.854218921101000.16390.16220.1973RANDOM14.28
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]
0.78-0.76-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.884
r_dihedral_angle_3_deg12.367
r_dihedral_angle_4_deg10.635
r_dihedral_angle_1_deg5.308
r_scangle_it5.024
r_scbond_it3.458
r_mcangle_it2.433
r_angle_refined_deg1.65
r_mcbond_it1.511
r_chiral_restr0.133
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.884
r_dihedral_angle_3_deg12.367
r_dihedral_angle_4_deg10.635
r_dihedral_angle_1_deg5.308
r_scangle_it5.024
r_scbond_it3.458
r_mcangle_it2.433
r_angle_refined_deg1.65
r_mcbond_it1.511
r_chiral_restr0.133
r_bond_refined_d0.024
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2732
Nucleic Acid Atoms
Solvent Atoms258
Heterogen Atoms70

Software

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