2QDM

Crystal structure of the HePTP catalytic domain C270S/D236A/Q314A mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62771.5 M AMMONIUM CHLORIDE, 0.1 M SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3848.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.324α = 90
b = 39.041β = 124.53
c = 83.473γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Si(111) CHANNEL CUT MONOCHROMATOR, TOROIDAL FOCUSING MIRROR2007-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C1.1000NSLSX12C

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
12.055099.10.04626.93.3200651988411
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)
12.052.1292.80.122.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1ZC02.05201915319016102399.420.166360.164070.20821RANDOM22.635
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]
1.270.91-0.17-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.79
r_dihedral_angle_4_deg17.286
r_dihedral_angle_3_deg13.129
r_dihedral_angle_1_deg10.079
r_scangle_it6.796
r_scbond_it4.692
r_mcangle_it2.979
r_mcbond_it1.976
r_angle_refined_deg1.465
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.79
r_dihedral_angle_4_deg17.286
r_dihedral_angle_3_deg13.129
r_dihedral_angle_1_deg10.079
r_scangle_it6.796
r_scbond_it4.692
r_mcangle_it2.979
r_mcbond_it1.976
r_angle_refined_deg1.465
r_nbtor_refined0.305
r_nbd_refined0.203
r_symmetry_vdw_refined0.158
r_xyhbond_nbd_refined0.156
r_chiral_restr0.101
r_symmetry_hbond_refined0.09
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2242
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms10

Software

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