X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details PROTEIN (10MG/ML) + DNA (4MG/ML) WAS CRYSTALLISED FROM 40% MPD, 100MM SODIUM CACODYLATE BUFFER, PH 7.0.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 118.39 α = 90
b = 118.39 β = 90
c = 83.71 γ = 120
Symmetry
Space Group P 62 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC MIRRORS 1997-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
3.4 30 99.3 0.085 -- -- 4.0 -- 19851 -- 3.0 9.8
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)
3.4 3.58 100.0 0.085 0.231 3.3 4.1 --

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 3.4 30.0 -- 0.0 -- 4864 480 95.2 -- 0.226 0.226 0.309 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 3.4 3.48 -- 43 279 0.313 0.347 0.053 94.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model GROUP
Mean Isotropic B 72.8
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 1.11
x_dihedral_angle_d 24.3
x_angle_deg 1.6
x_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.42
Luzzati Sigma A (Observed) 0.46
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.56
Luzzati Sigma A (R-Free Set) 0.71
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1690
Nucleic Acid Atoms 382
Heterogen Atoms 0
Solvent Atoms 0

Software

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