X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.2
Details CRYSTALS WERE PREPARED AT 277K FROM A SOLUTION CONTAINING 20 MG/ML PROTEIN, 7 MM TRI-N-ACETYLCHITOTRIOSE, 25 MG/ML SODIUM CHLORIDE, AND 100 MM ACETATE BUFFER PH 4.2, BY EQUILIBRATING THE SOLUTION AGAINST A RESERVOIR SOLUTION CONTAINING 50 MG/ML SODIUM CHLORIDE AND 100 MM ACETATE BUFFER PH 4.2.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.61 α = 90
b = 78.61 β = 90
c = 38.78 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 277
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU MIRRORS 1996-05
Diffraction Radiation
Monochromator Protocol
NI FILTER --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R -- -- --

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
1.8 34.8 92.3 0.052 -- -- 5.2 -- 10924 -- 0.0 21.1
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)
1.8 1.83 65.2 -- -- -- -- --

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 1.8 8.0 -- 0.0 -- 10754 1071 92.8 -- 0.182 0.182 0.233 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 1.8 1.86 -- 89 668 0.233 0.277 0.029 65.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 20.8
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 4.61
x_scbond_it 2.93
x_mcangle_it 2.44
x_mcbond_it 1.54
x_improper_angle_d 1.28
x_bond_d 0.01
x_angle_deg 1.35
x_dihedral_angle_d 23.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.19
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1000
Nucleic Acid Atoms 0
Heterogen Atoms 45
Solvent Atoms 95

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR 3.843 Structure Solution
X-PLOR 3.843 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.843 refinement
X-PLOR version: 3.843 model building
SCALEPACK data reduction
DENZO data collection