X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Under Oil
pH 7.5
Details CRYSTALS GROWN UNDER OIL IN TERASAKI PLATES. DROPS FORMED FROM A 1:1 MIXTURE OF PROTEIN/DNA COMPLEX (10MG/ML COMPLEX, 20MM TRIS PH 7.5, 1MM EDTA, 0.1M NACL, 15% GLYCEROL) AND 1.4M NACITRATE, 0.1M TRIS PH 7.5., under oil

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 142.63 α = 90
b = 142.63 β = 90
c = 108.35 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1997-11-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX7.2 -- SRS PX7.2

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 38.4 99.6 -- 0.056 -- 2.8 -- 49353 -- -- 82.1
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)
2.99 3.15 99.6 -- 0.218 3.3 2.7 --

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 3.0 30.0 -- 1.0 -- 49126 2490 99.7 -- 0.274 0.274 0.319 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 3.0 3.19 -- 376 7665 0.385 0.443 0.023 98.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model GROUP
Mean Isotropic B 46.2
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 0.78
x_bond_d 0.013
x_angle_deg 1.9
x_dihedral_angle_d 26.1
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.44
Luzzati Sigma A (Observed) 0.66
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.51
Luzzati Sigma A (R-Free Set) 0.77
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10448
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
AMORE model building