X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 10% PEG 8000, 100mM Tris-Cl pH=8.0, 10mM NaCl, 20mM Cacl2, 2mM NaN3. Protein solution: 5mg/ml in 10mM Tris-Cl pH=8.0, 10 mM NaCl, 20mM CaCl2, 1.1mM Man6GlcNAc2Asn. VAPOR DIFFUSION, HANGING DROP at 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.8 α = 90
b = 255.56 β = 119.6
c = 61.79 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC -- 1995-12-08
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

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
2.8 50 94.4 -- 0.044 -- -- 40098 37844 -- -3.0 --
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)
2.8 2.93 75.9 -- 0.163 -- -- --

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 2.8 37.04 -- 0.0 36749 36749 3452 91.1 -- 0.242 0.242 0.287 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 2.8 -- -- -- 4118 -- -- -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 38.4
Anisotropic B[1][1] -0.74
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 8.44
Anisotropic B[2][2] 2.63
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.89
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 2.03
c_scangle_it 3.06
c_angle_deg 1.3
c_dihedral_angle_d 22.3
c_mcangle_it 2.31
c_improper_angle_d 0.81
c_bond_d 0.007
c_mcbond_it 1.39
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.4
Luzzati Sigma A (Observed) 0.47
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.49
Luzzati Sigma A (R-Free Set) 0.6
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6918
Nucleic Acid Atoms 0
Heterogen Atoms 176
Solvent Atoms 45

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS refinement
CNS phasing