X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details 0.2 M POTASSIUM CHLORIDE, 0.1 M MAGNESIUM ACETATE, 10.0% W/V PEG 8000, 0.05 M SODIUM CACODYLATE CACODYLATE BUFFER PH 6.5, PROTEIN-DNA COMPLEX SOLUTION CONTAINS 0.01 M DTT AND 0.005 M NAN3, PROTEIN:DNA RATIO IS 1:1.2

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.94 α = 90
b = 112.53 β = 90
c = 74.35 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RAXIS IV RIGAKU -- 1998-12-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44B2 -- SPRING-8 BL44B2

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
1.7 20 95.8 0.052 -- -- 4.008 -- 44759 -- 0.0 34.2
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)
1.7 1.76 82.9 0.43 -- 1.343 2.43 --

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 1.85 19.87 -- 0.0 -- 35717 1809 98.0 -- 0.231 0.231 0.271 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 1.85 1.97 -- 282 5402 0.378 0.432 0.026 94.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 42.9
Anisotropic B[1][1] 7.95
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.79
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 9.23
c_scbond_it 6.94
c_mcangle_it 5.68
c_mcbond_it 4.97
c_improper_angle_d 1.13
c_bond_d 0.004
c_angle_deg 1.0
c_dihedral_angle_d 15.7
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.27
Luzzati Sigma A (Observed) 0.39
Luzzati Resolution Cutoff (Low) 20.0
Luzzati ESD (R-Free Set) 0.32
Luzzati Sigma A (R-Free Set) 0.44
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1129
Nucleic Acid Atoms 650
Heterogen Atoms 0
Solvent Atoms 316

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
X-PLOR model building