X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS727810 mg protein/ml dialyzed against 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfonate buffer, pH 7 (pH 6.7 at 25 deg C) with 1 mM NADH and 10 mM (racemic) (R,S)-N-1-methylhexylformamide as the concentration of 2-methyl-2,4-pentanediol was raised to 25%. Crystal on loop plunged into liquid N2.
Crystal Properties
Matthews coefficientSolvent content
2.3848.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.212α = 90
b = 180.808β = 106.12
c = 86.841γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm1999-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.936ESRFID14-4

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
11.22083.80.1220.1515.771.762386016-3
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)
11.21.2567.50.3180.4262.21.518

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 REPLACEMENTTHROUGHOUT1p1r1.2520325043165080.010.15170.15150.1866RANDOM25.461
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]
1.710.28-1.4-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.372
r_sphericity_free18.984
r_dihedral_angle_4_deg14.312
r_dihedral_angle_3_deg11.536
r_sphericity_bonded7.418
r_dihedral_angle_1_deg6.276
r_rigid_bond_restr2.976
r_angle_refined_deg1.885
r_angle_other_deg1.063
r_chiral_restr0.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.372
r_sphericity_free18.984
r_dihedral_angle_4_deg14.312
r_dihedral_angle_3_deg11.536
r_sphericity_bonded7.418
r_dihedral_angle_1_deg6.276
r_rigid_bond_restr2.976
r_angle_refined_deg1.885
r_angle_other_deg1.063
r_chiral_restr0.122
r_bond_refined_d0.017
r_gen_planes_refined0.01
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 Atoms1329
Heterogen Atoms250

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
X-PLORphasing
Omodel building