X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4RKIPDB ENTRY 4RKI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16% W/V PEG 20,000, 20% V/V PEG 550MME, 0.01M MGCL2, 0.1M MOPS/ HEPES-NA PH7.3, 0.2M AMMONIUM CITRATE
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.311α = 90
b = 66.372β = 115.96
c = 89.119γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray287CCDMARRESEARCH2015-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.2880.1399.10.0815.13.9393850.3
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)
12.2880.1393.60.681.92.8

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 4RKI2.2833.1937427194498.680.235580.234580.25475RANDOM41.864
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]
-2.72-6.015.48-2.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.089
r_dihedral_angle_3_deg14.301
r_dihedral_angle_4_deg12.037
r_dihedral_angle_1_deg6.363
r_mcangle_it1.493
r_angle_refined_deg1.169
r_angle_other_deg0.825
r_mcbond_it0.799
r_mcbond_other0.799
r_scbond_it0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.089
r_dihedral_angle_3_deg14.301
r_dihedral_angle_4_deg12.037
r_dihedral_angle_1_deg6.363
r_mcangle_it1.493
r_angle_refined_deg1.169
r_angle_other_deg0.825
r_mcbond_it0.799
r_mcbond_other0.799
r_scbond_it0.48
r_chiral_restr0.065
r_bond_refined_d0.007
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5897
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement