4NCY

In situ trypsin crystallized on a MiTeGen micromesh with imidazole ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4I8GPDB ENTRY 4I8G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1In situ crystallization on micromesh727730mg/ml+10mg/ml Benzenmidine in 20mM HEPES pH 7 and 10mM CaCl2; precipitant is 20% PEG 8000 + 200mM AmSO4 + 100mM Bis-Tris, In situ crystallization on micromesh, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2545.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.392α = 90
b = 58.186β = 90
c = 66.43γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.1NSLSX25

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
11.4243.7799.860.04346.315.9382083815521
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)
11.4299.860.04346.315.938208

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 4I8G1.4243.7738155201299.860.119150.118110.13849RANDOM10.881
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]
0.08-0.320.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.428
r_dihedral_angle_4_deg18.087
r_dihedral_angle_3_deg11.279
r_dihedral_angle_1_deg7.133
r_long_range_B_refined6.72
r_long_range_B_other5.815
r_scangle_other3.268
r_angle_refined_deg2.785
r_scbond_it2.309
r_scbond_other2.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.428
r_dihedral_angle_4_deg18.087
r_dihedral_angle_3_deg11.279
r_dihedral_angle_1_deg7.133
r_long_range_B_refined6.72
r_long_range_B_other5.815
r_scangle_other3.268
r_angle_refined_deg2.785
r_scbond_it2.309
r_scbond_other2.308
r_mcangle_it1.526
r_mcangle_other1.526
r_angle_other_deg1.067
r_mcbond_it1.048
r_mcbond_other1.048
r_chiral_restr0.15
r_bond_refined_d0.028
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1629
Nucleic Acid Atoms
Solvent Atoms417
Heterogen Atoms64

Software

Software
Software NamePurpose
CBASSdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling