X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YPM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION6.52950.2M sodium citrate pH6.5, 12% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.7655.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.309α = 90
b = 212.787β = 100.8
c = 178.921γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDRAYONIX MX-3252014-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A10.8NSRRCBL15A1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.03175.890.9216.74.774605
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)
13.053.1693.80.72.334.7

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 REPLACEMENTTHROUGHOUT4YPM3.032070806379890.50.230.2270.279RANDOM72.18
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]
0.080.63-0.650.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.564
r_dihedral_angle_3_deg17.523
r_dihedral_angle_4_deg13.642
r_dihedral_angle_1_deg5.247
r_long_range_B_refined2.774
r_long_range_B_other2.774
r_mcangle_it1.593
r_mcangle_other1.593
r_angle_refined_deg0.947
r_scangle_other0.916
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.564
r_dihedral_angle_3_deg17.523
r_dihedral_angle_4_deg13.642
r_dihedral_angle_1_deg5.247
r_long_range_B_refined2.774
r_long_range_B_other2.774
r_mcangle_it1.593
r_mcangle_other1.593
r_angle_refined_deg0.947
r_scangle_other0.916
r_mcbond_it0.844
r_mcbond_other0.844
r_angle_other_deg0.722
r_scbond_it0.421
r_scbond_other0.421
r_chiral_restr0.051
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms26292
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building