X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE4.729440MG HEWL CO-CRYSTALLISED WITH 2.6MG CISPLATIN, WITH THE PLATINUM COMPOUNDS BEING IN A 3-FOLD MOLAR EXCESS TO THE PROTEIN. 462.5 MicroL OF A 0.02M NAAC SOLUTION ALONG WITH 462.5 MicroL OF A 0.5M NANO3 SOLUTION WAS USED WITH 75 MicroL DMSO ADDED, BATCH, PH 4.7, EVAPORATION, TEMPERATURE 294K
Crystal Properties
Matthews coefficientSolvent content
1.831.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 26.998α = 89.08
b = 31.807β = 72
c = 34.072γ = 67.81
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray150CCDAPEX II CCD2012-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
10.9829.2894.80.04515.63.548959
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)
10.981.0249.70.2093.20.6

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 REPLACEMENTTHROUGHOUT4mwk0.9829.2848959264690.560.124890.123720.14652RANDOM7.87
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]
0.080.040.10.07-0.05-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.34
r_dihedral_angle_4_deg13.582
r_sphericity_free13.159
r_dihedral_angle_3_deg10.416
r_rigid_bond_restr9.813
r_dihedral_angle_1_deg6.761
r_sphericity_bonded5.291
r_long_range_B_refined2.291
r_long_range_B_other2.29
r_scangle_other2.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.34
r_dihedral_angle_4_deg13.582
r_sphericity_free13.159
r_dihedral_angle_3_deg10.416
r_rigid_bond_restr9.813
r_dihedral_angle_1_deg6.761
r_sphericity_bonded5.291
r_long_range_B_refined2.291
r_long_range_B_other2.29
r_scangle_other2.2
r_scbond_it2.062
r_scbond_other2.061
r_angle_refined_deg1.975
r_mcangle_it1.08
r_mcangle_other1.079
r_angle_other_deg0.945
r_mcbond_it0.863
r_mcbond_other0.862
r_chiral_restr0.142
r_bond_refined_d0.023
r_gen_planes_refined0.012
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms992
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SAINTdata scaling
PHASERphasing