X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.6
Details NC10 SCFV(15) AND N9 NA WERE MIXED TOGETHER (SCFV(15) IN SLIGHT MOLAR EXCESS) WITH AND EQUAL VOLUME OF POTASSIUM PHOSPHATE BUFFER 1.7M PH6.6. THE DROP WAS EQUILIBRATED BY VAPOUR DIFFUSION AGAINST PHOSPHATE BUFFER 1.3M PH6.8.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 144.4 α = 90
b = 144.4 β = 90
c = 227 γ = 90
Symmetry
Space Group P 4 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 287
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE AREA DETECTOR PHOTON FACTORY -- 1995-07
Diffraction Radiation
Monochromator Protocol
-- --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A -- PHOTON FACTORY BL-6A

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
2.5 -- 80.0 0.104 -- -- -- -- 67425 -- 2.0 34.0
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)
2.5 2.6 70.0 -- -- -- -- --

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 2.5 7.0 -- 2.0 -- 64026 -- 80.0 -- 0.22 0.22 0.26 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 2.5 2.65 -- -- 9223 0.36 -- -- 70.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.0
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 1.47
x_bond_d 0.011
x_angle_deg 1.9
x_dihedral_angle_d 26.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Sigma A (Observed) 0.5
Luzzati Resolution Cutoff (Low) 5.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9734
Nucleic Acid Atoms 0
Heterogen Atoms 224
Solvent Atoms 180

Software

Computing
Computing Package Purpose
WEIS Data Reduction (intensity integration)
PROTEIN Data Reduction (data scaling)
X-PLOR 3.1 Structure Solution
X-PLOR 3.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.1 refinement
X-PLOR version: 3.1 model building
PROTEIN data reduction
WEIS data collection