4LAK

Crystal structure of Cordyceps militaris IDCase D323N mutant in apo form


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, 0.2 M MgCl2, 0.1 M Tris-HCl, pH 8.5, sitting drop, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.5952.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.618α = 90
b = 77.618β = 90
c = 140.089γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2012-12-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9792SSRFBL17U

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
12.477.6297.10.1039.53.531075
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)
12.42.4998.40.6563.53125

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 REPLACEMENTTHROUGHOUT4HK52.415031074158097.010.18380.18070.2399RANDOM57.078
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]
0.720.72-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded34.311
r_dihedral_angle_2_deg33.137
r_sphericity_free29.559
r_dihedral_angle_3_deg13.886
r_dihedral_angle_4_deg12.601
r_dihedral_angle_1_deg4.222
r_rigid_bond_restr1.123
r_angle_refined_deg0.975
r_chiral_restr0.063
r_bond_refined_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded34.311
r_dihedral_angle_2_deg33.137
r_sphericity_free29.559
r_dihedral_angle_3_deg13.886
r_dihedral_angle_4_deg12.601
r_dihedral_angle_1_deg4.222
r_rigid_bond_restr1.123
r_angle_refined_deg0.975
r_chiral_restr0.063
r_bond_refined_d0.005
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5339
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms2

Software

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