4YEO

Triclinic HEWL co-crystallised with cisplatin, studied at a data collection temperature of 150K - new refinement


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION4.729440mg HEWL co-crystallised with 2.6mg cisplatin, with the platinum compounds being in a 3-fold molar excess to the protein. 462.5 ul of a 0.02M NaAc solution along with 462.5 ul of a 0.5M NaNo3 solution was used with 75 ul DMSO added
Crystal Properties
Matthews coefficientSolvent content
1.8931.34

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)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
10.9829.2894.80.0450.04515.63.54895926
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)
10.981.0251.70.2093.20.6

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4mwk0.9829.2648959264690.560.11330.11230.1313RANDOM7.982
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]
0.080.020.120.09-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.998
r_dihedral_angle_4_deg13.767
r_sphericity_free11.165
r_dihedral_angle_3_deg10.707
r_dihedral_angle_1_deg6.627
r_sphericity_bonded6.316
r_rigid_bond_restr5.396
r_angle_refined_deg1.711
r_angle_other_deg1.358
r_mcangle_it0.948
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.998
r_dihedral_angle_4_deg13.767
r_sphericity_free11.165
r_dihedral_angle_3_deg10.707
r_dihedral_angle_1_deg6.627
r_sphericity_bonded6.316
r_rigid_bond_restr5.396
r_angle_refined_deg1.711
r_angle_other_deg1.358
r_mcangle_it0.948
r_mcbond_it0.695
r_mcbond_other0.694
r_chiral_restr0.103
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms997
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
APEXdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction