X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ONRPDB entry 1ONR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52944M sodium formate, 3mM magnesium chloride, cryoprotected in Paratone-N oil (Hampton), VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
4.8874.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.105α = 90
b = 143.105β = 90
c = 119.724γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rMirrors2009-06-27MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97942, 0.97972APS19-BM

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
12.835.7899.90.0880.08857.426.21848418469-3
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)
12.82.998.90.7340.7344.925.8

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 1ONR2.7935.781747594799.820.211140.209140.24886RANDOM71.242
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]
0.040.020.04-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.726
r_dihedral_angle_4_deg23.341
r_dihedral_angle_3_deg20.289
r_dihedral_angle_1_deg6.614
r_angle_refined_deg1.468
r_nbtor_refined0.322
r_symmetry_vdw_refined0.3
r_nbd_refined0.257
r_xyhbond_nbd_refined0.168
r_chiral_restr0.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.726
r_dihedral_angle_4_deg23.341
r_dihedral_angle_3_deg20.289
r_dihedral_angle_1_deg6.614
r_angle_refined_deg1.468
r_nbtor_refined0.322
r_symmetry_vdw_refined0.3
r_nbd_refined0.257
r_xyhbond_nbd_refined0.168
r_chiral_restr0.098
r_symmetry_hbond_refined0.065
r_bond_refined_d0.014
r_gen_planes_refined0.005
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2503
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms

Software

Software
Software NamePurpose
SBC-Collectdata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-2000data scaling