X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XA8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52890.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP, 50mM D-lactate, and 5 mM NADPH were mixed with 0.2 ul of the MCSG-2 condition #13 (0.1M MES monohydrate pH=6.5, 12%w/v PEG 20K) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 1 mg/ml TEV solution at 289 K for 1 hour
Crystal Properties
Matthews coefficientSolvent content
2.7455.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.514α = 90
b = 311.036β = 90
c = 98.977γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9793APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim 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
12.2501000.1140.1140.1280.0550.85.15.3207487-335.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.241000.7530.7530.850.3890.8011.94.7

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 REPLACEMENTTHROUGHOUT4XA82.2501969741034399.90.20130.19960.2334RANDOM57.011
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]
-0.491.05-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.544
r_dihedral_angle_4_deg12.95
r_dihedral_angle_3_deg12.303
r_dihedral_angle_1_deg5.014
r_angle_refined_deg1.334
r_angle_other_deg1.251
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.544
r_dihedral_angle_4_deg12.95
r_dihedral_angle_3_deg12.303
r_dihedral_angle_1_deg5.014
r_angle_refined_deg1.334
r_angle_other_deg1.251
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms22504
Nucleic Acid Atoms
Solvent Atoms2680
Heterogen Atoms588

Software

Software
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling