X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P1R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS727810 mg/ml enzyme dialyzed against 50 mM ammonium N-[tris(hydroxylmethyl)methyl]2-aminoethane sulfonate (pH 6.7 at 25 deg C) with 1 mM NADH and 10 mM N-benzylformamide as the concentration of 2-methyl-2,4-pentanediol was raised to 25 %. Crystas was mounted on a fiber loop and flash vitrified by plunging it into liquid N2.
Crystal Properties
Matthews coefficientSolvent content
2.3748.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.16α = 90
b = 180.29β = 106.18
c = 86.92γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.000APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.219.9579.40.0880.0948.36.19365139
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2459.50.5130.5761.74.34

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT1P1R1.219.95361271377579.390.15860.15820.1985RANDOM20.318
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]
1.630.19-1.760.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.882
r_sphericity_free19.85
r_dihedral_angle_4_deg14.777
r_dihedral_angle_3_deg11.714
r_sphericity_bonded6.595
r_dihedral_angle_1_deg6.266
r_rigid_bond_restr3.996
r_angle_refined_deg2.061
r_angle_other_deg1.089
r_chiral_restr0.128
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.882
r_sphericity_free19.85
r_dihedral_angle_4_deg14.777
r_dihedral_angle_3_deg11.714
r_sphericity_bonded6.595
r_dihedral_angle_1_deg6.266
r_rigid_bond_restr3.996
r_angle_refined_deg2.061
r_angle_other_deg1.089
r_chiral_restr0.128
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11140
Nucleic Acid Atoms
Solvent Atoms1357
Heterogen Atoms240

Software

Software
Software NamePurpose
d*TREKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Omodel building
d*TREKdata reduction