X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NQOpdb entry 2NQO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5292200 MM HEPES, 25% PEG MME2000, 5 MG/ML PROTEIN, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.1743.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.983α = 90
b = 104.762β = 91.85
c = 91.91γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.65099.40.0750.08821.96.5136302
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6699.30.3840.4742.74.9

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 REPLACEMENTTHROUGHOUTpdb entry 2NQO1.632.931223211349499.270.168880.166520.19017RANDOM15.361
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]
-0.07-0.030.42-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.347
r_dihedral_angle_4_deg16.006
r_dihedral_angle_3_deg11.737
r_dihedral_angle_1_deg6.113
r_scangle_it2.741
r_scbond_it1.737
r_angle_refined_deg1.228
r_mcangle_it0.939
r_mcbond_it0.633
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.347
r_dihedral_angle_4_deg16.006
r_dihedral_angle_3_deg11.737
r_dihedral_angle_1_deg6.113
r_scangle_it2.741
r_scbond_it1.737
r_angle_refined_deg1.228
r_mcangle_it0.939
r_mcbond_it0.633
r_nbtor_refined0.303
r_nbd_refined0.194
r_symmetry_vdw_refined0.148
r_symmetry_hbond_refined0.119
r_xyhbond_nbd_refined0.104
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8050
Nucleic Acid Atoms
Solvent Atoms737
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing