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_improper_angle_d 1.26
x_dihedral_angle_d 24.4
x_bond_d 0.007
x_angle_deg 1.2
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

Software
Software Name Purpose
AMoRE phasing
X-PLOR refinement version: 3.860
MOSFLM data reduction
CCP4 data scaling