4LAM

Crystal structure of Cordyceps militaris IDCase D323N mutant in complex with 5-carboxyl-uracil


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HK5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1sitting drop8.528925% polyethylene glycol 3350, 0.2M MgCl2, 0.1M Tris-HCl, pH 8.5, sitting drop, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4750.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.361α = 90
b = 77.361β = 90
c = 134.421γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2013-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9793SSRFBL17U

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
12.15099.90.08511.73.846222
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)
12.12.181000.2323.84573

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 REPLACEMENTTHROUGHOUT4HK52.138.846175234099.670.16090.15930.19RANDOM32.6788
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]
0.140.14-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.405
r_sphericity_free16.45
r_dihedral_angle_4_deg14.077
r_dihedral_angle_3_deg13.425
r_sphericity_bonded11.391
r_dihedral_angle_1_deg4.997
r_rigid_bond_restr2.448
r_mcbond_it1.527
r_mcbond_other1.527
r_mcangle_it1.524
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.405
r_sphericity_free16.45
r_dihedral_angle_4_deg14.077
r_dihedral_angle_3_deg13.425
r_sphericity_bonded11.391
r_dihedral_angle_1_deg4.997
r_rigid_bond_restr2.448
r_mcbond_it1.527
r_mcbond_other1.527
r_mcangle_it1.524
r_angle_other_deg1.468
r_angle_refined_deg1.083
r_chiral_restr0.062
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5590
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms70

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing