X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YOR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429120% PEG 3350, 0.2 M ammonium nitrate, 0.1 M Sodium acetate pH 4.0
Crystal Properties
Matthews coefficientSolvent content
2.4549.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.999α = 90
b = 99.151β = 103.27
c = 83.89γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB mirrors2014-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.9795ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.4245.2397.90.99819.26.8190184
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.421.4490.40.9726.85.5

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 REPLACEMENTTHROUGHOUT2YOR1.4245.23180609954197.770.151010.150310.16423RANDOM12.45
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]
-0.15-0.29-0.210.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.232
r_dihedral_angle_4_deg17.229
r_dihedral_angle_3_deg12.114
r_dihedral_angle_1_deg5.666
r_long_range_B_refined3.774
r_long_range_B_other3.465
r_angle_refined_deg1.331
r_scangle_other1.278
r_angle_other_deg0.956
r_mcangle_it0.914
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.232
r_dihedral_angle_4_deg17.229
r_dihedral_angle_3_deg12.114
r_dihedral_angle_1_deg5.666
r_long_range_B_refined3.774
r_long_range_B_other3.465
r_angle_refined_deg1.331
r_scangle_other1.278
r_angle_other_deg0.956
r_mcangle_it0.914
r_mcangle_other0.914
r_scbond_it0.782
r_scbond_other0.782
r_mcbond_it0.527
r_mcbond_other0.526
r_chiral_restr0.077
r_gen_planes_other0.008
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7590
Nucleic Acid Atoms
Solvent Atoms1282
Heterogen Atoms345

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing