X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NPDpdb entry 1NPD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5295Protein: 7.5mG/mL, 0.25M Sodium chloride, 0.01M TRIS-HCl (pH 8.3); Screen: Classics II (F8), 0.2M Ammonium sulfate, 0.1M HEPES (pH 7.5), 25% (w/v) PEG R3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1141.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.13α = 90
b = 78.434β = 90.49
c = 214.829γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium lenses2011-07-14MSINGLE 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)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
12.23098.20.09612.33.8117864117864-337
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)
12.22.2497.30.5252.53.95755

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1NPD2.229.63110577110577583698.180.198550.198550.195470.25584RANDOM33.413
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]
-3.3-2.454.26-1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.159
r_dihedral_angle_4_deg11.626
r_dihedral_angle_3_deg9.635
r_scangle_it4.281
r_scbond_it2.951
r_dihedral_angle_1_deg2.274
r_mcangle_it1.634
r_angle_refined_deg1.568
r_mcbond_it0.97
r_angle_other_deg0.856
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.159
r_dihedral_angle_4_deg11.626
r_dihedral_angle_3_deg9.635
r_scangle_it4.281
r_scbond_it2.951
r_dihedral_angle_1_deg2.274
r_mcangle_it1.634
r_angle_refined_deg1.568
r_mcbond_it0.97
r_angle_other_deg0.856
r_mcbond_other0.297
r_chiral_restr0.089
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17938
Nucleic Acid Atoms
Solvent Atoms1010
Heterogen Atoms396

Software

Software
Software NamePurpose
Blu-Icedata collection
BALBESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling