X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YNPPDB ENTRY 1YNP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429310mM NADP+ 25.5% of polyacrylic acid 0.1M Hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2545.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.17α = 90
b = 120.277β = 90
c = 151.113γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.873ESRFID23-2

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
12.894.1197.20.1290.1298.94.141558
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)
12.82.9598.20.4932.74.1

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1YNP2.894.113943339433210296.630.229490.227230.27237RANDOM22.901
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]
-0.11-0.010.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.373
r_dihedral_angle_3_deg18.773
r_dihedral_angle_4_deg17.898
r_dihedral_angle_1_deg6.54
r_scangle_it2.637
r_scbond_it1.428
r_angle_refined_deg1.345
r_mcangle_it1.107
r_angle_other_deg0.942
r_mcbond_it0.575
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.373
r_dihedral_angle_3_deg18.773
r_dihedral_angle_4_deg17.898
r_dihedral_angle_1_deg6.54
r_scangle_it2.637
r_scbond_it1.428
r_angle_refined_deg1.345
r_mcangle_it1.107
r_angle_other_deg0.942
r_mcbond_it0.575
r_mcbond_other0.089
r_chiral_restr0.068
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11626
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms216

Software

Software
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling