X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Details THE PROTEIN WAS CRYSTALLIZED IN 21% PEG 6000, 100 MM SODIUM CITRATE PH 4.5, IN HANGING DROPS CONTAINING SUBTILISIN CARLSBERG IN A 1:100 MOLAR RATIO., vapor diffusion - hanging drop THE DEPOSITORS CRYSTALLIZED THE SINGLE CHAIN FV IN THE PRESENCE OF SUBTILISIN, AS DESCRIBED IN THE PRIMARY REFERENCE. THE SEQUENCE OF THE SINGLE CHAIN IS DIVMTQSPSSLTVTAGEKVTMSCKSSQSLLNSGNQKNYLTWYQQKPGQPPKLLIYWAS TRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCQNDYSYPLTFGAGTKLEP (LIGHT CHAINS A AND C) GGGGSGGGGSGKSGGGG (LINKER) EVQLQQSGAELVRPGASVKLSCTASGFNIKDDFMHWVKQRPEQGLEWIGRIDPANDNT KYAPKFQDKATIIADTSSNTAYLQLSSLTSEDTAVYYCARREVYSYYSPLDVWGAGTT VTVPSG (HEAVY CHAINS B AND D) SEQKLISEEDLNHHHHH (C-MYC TAG + 5XHIS TAG) THE DEPOSITORS HAVE NOT DETERMINED WHERE SUBTILISIN CLEAVES EXACTLY, BUT THE MOBILITY ON SDS GELS SUGGESTS THAT THE MOST OF THE LINKER AND MOST OF BOTH TAGS ARE REMOVED.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.04 α = 90
b = 64.35 β = 90
c = 154.11 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR XUONG-HAMLIN MULTIWIRE -- 1997-05
Diffraction Radiation
Monochromator Protocol
QUARTZ CRYSTAL --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU -- -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.36 50 91.6 -- 0.098 -- 3.6 -- 22616 -- 2.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.36 2.55 76.1 -- 0.277 2.8 2.3 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.36 6.0 -- 2.0 -- 19352 1519 78.4 -- 0.2045 0.2045 0.284 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.36 2.46 -- 91 1109 0.2584 0.3798 0.039 --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED (GAUSSIAN)
Mean Isotropic B 10.77
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 0.572
x_bond_d 0.006
x_dihedral_angle_d 30.29
x_scangle_it 2.931
x_scbond_it 2.957
x_mcangle_it 8.01
x_angle_deg 1.121
x_mcbond_it 6.343
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3618
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 102

Software

Computing
Computing Package Purpose
SDMS Data Reduction (intensity integration)
SDMS Data Reduction (data scaling)
X-PLOR 3.851 Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
SDMS data reduction
SDMS data collection
X-PLOR version: 3.851 model building