2PEF

Crystal Structure of a Thermophilic Serpin, Tengpin, in the Latent State


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SNGPDB ENTRY 1SNG, THERMOPIN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.529428% PEG 400, 0.1 M Na Hepes, 0.2 M Calcium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
1.8935.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.762α = 90
b = 44.907β = 90
c = 159.233γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-CAPS14-BM-C

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
11.67998.40.07620.15.4427973
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)
11.61.6698.10.3511.61.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1SNG, THERMOPIN1.67940547213898.50.2080.2060.253RANDOM17.58
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]
-0.080.23-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.556
r_dihedral_angle_4_deg13.638
r_dihedral_angle_3_deg11.854
r_dihedral_angle_1_deg5.091
r_scangle_it3.036
r_scbond_it2.202
r_mcangle_it1.281
r_angle_refined_deg0.999
r_mcbond_it0.799
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.556
r_dihedral_angle_4_deg13.638
r_dihedral_angle_3_deg11.854
r_dihedral_angle_1_deg5.091
r_scangle_it3.036
r_scbond_it2.202
r_mcangle_it1.281
r_angle_refined_deg0.999
r_mcbond_it0.799
r_nbtor_refined0.3
r_nbd_refined0.178
r_symmetry_vdw_refined0.155
r_xyhbond_nbd_refined0.099
r_symmetry_hbond_refined0.089
r_chiral_restr0.072
r_bond_refined_d0.006
r_gen_planes_refined0.003
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 Atoms2841
Nucleic Acid Atoms
Solvent Atoms484
Heterogen Atoms

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling