X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details PROTEIN (10MG/ML) + SAM(1.5MG/ML) + DNA (4MG/ML) WAS CRYSTALLISED FROM 28-38% MPD, 100MM SODIUM CACODYLATE BUFFER, PH 6.0-7.0, 40MM CACL2

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 119.42 α = 90
b = 119.42 β = 90
c = 84.83 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH RHODIUM COATED MIRROR 1997-04
Diffraction Radiation
Monochromator Protocol
SILICON (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID2 -- ESRF ID2

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
2.4 27.17 97.8 0.046 -- -- 2.4 -- 125697 -- 0.0 40.8
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)
2.4 2.53 97.8 0.046 0.197 3.7 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
DIFFERENCE FOURIER METHODS 2.4 27.3 -- 0.0 -- 45112 2538 85.3 -- 0.223 0.223 0.268 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 2.4 2.46 -- 124 1857 0.383 0.503 0.045 56.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 62.4
RMS Deviations
Key Refinement Restraint Deviation
x_bond_d 0.007
x_angle_deg 1.2
x_dihedral_angle_d 24.4
x_improper_angle_d 1.26
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.38
Luzzati Sigma A (Observed) 0.57
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.43
Luzzati Sigma A (R-Free Set) 0.64
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6760
Nucleic Acid Atoms 1544
Heterogen Atoms 216
Solvent Atoms 186

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 Data Reduction (data scaling)
AMORE Structure Solution
X-PLOR 3.860 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.860 refinement
AMORE model building