X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5
Details PROTEIN WAS CRYSTALLIZED BY SITTING DROP TECHNIQUE IN THE COLD ROOM (8 DEGREES C +/- 2 DEGREES C) BY MIXING 4 MICROLITERS OF 1 MM PROTEIN CONTAINING 1.2-1.5 MM TFP IN 5 MM CACL2 WITH 4 MICROLITERS OF THE RESERVOIR SOLUTION (1 ML 10 MM SODIUM CACODYLATE/HCL BUFFER, PH 5.2-5.6 WITH 10 MM CACL2, 25-30 % (W/V) POLYETHYLENE GLYCOL 6000), CRYSTAL GROWTH TOOK 2-3 WEEKS., pH 5.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.75 α = 90
b = 40.75 β = 90
c = 177.57 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU NORMAL FOCUS 1995-02
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH2R -- -- --

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
2.74 87.7 98.0 0.086 0.0737 -- 1.92 -- 17223 -- 1.0 32.0
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)
2.74 2.86 98.2 0.092 0.205 1.84 1.9 --

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 2.74 59.19 -- 2.0 -- 4768 230 96.46 -- 0.1971 0.1971 0.265 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 2.74 2.82 -- 12 233 0.1661 0.3395 0.098 57.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model GROUPED
Mean Isotropic B 30.3
Anisotropic B[1][1] -9.975
Anisotropic B[1][2] -8.454
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -9.975
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.101
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 1.1
x_bond_d 0.006
x_angle_deg 1.08
x_dihedral_angle_d 21.5
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.27
Luzzati Sigma A (Observed) 0.12
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.4
Luzzati Sigma A (R-Free Set) 0.22
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1086
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 0

Software

Computing
Computing Package Purpose
BIOTEX Data Reduction (intensity integration)
BIOTEX 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
X-PLOR version: 3.851 model building