X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NZTpdb entry 2NZT, chain A, residues 468 through 913

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.2291reservoir solution: 16% PEG 3350, 0.20 M Ammonium Citrate, 0.1 M HEPES. 0.005 M glucose-6-phosphate, 0.005 M ADP-Mg, 0.02 M TCEP, 1:100 (w/w) trypsin was added to the protein stock solution., pH 7.2, vapor diffusion, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
358.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.904α = 90
b = 83.904β = 90
c = 323.327γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-03-20SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.82098.453686
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)
12.82.986.80.666

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMRpdb entry 2NZT, chain A, residues 468 through 9132.82052939150297.20.2450.2450.2769.23
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]
5.5415.541-11.082
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.612
r_dihedral_angle_4_deg12.304
r_dihedral_angle_3_deg11.488
r_dihedral_angle_1_deg3.864
r_angle_refined_deg1.054
r_angle_other_deg0.783
r_scangle_it0.576
r_scbond_it0.342
r_mcangle_it0.137
r_mcbond_it0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.612
r_dihedral_angle_4_deg12.304
r_dihedral_angle_3_deg11.488
r_dihedral_angle_1_deg3.864
r_angle_refined_deg1.054
r_angle_other_deg0.783
r_scangle_it0.576
r_scbond_it0.342
r_mcangle_it0.137
r_mcbond_it0.07
r_chiral_restr0.059
r_mcbond_other0.03
r_bond_refined_d0.011
r_bond_other_d0.003
r_gen_planes_refined0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12521
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms112

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction