X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details 0.08 M MAGNESIUM ACETATE, 15.0% V/V PEG 400, 0.05 M SODIUM CACODYLATE BUFFER PH 6.5, PROTEIN-DNA COMPLEX CONCENTRATION WAS 12 MG/ML WITH ADDITION OF 0.01 M DTT, PROTEIN:DNA RATIO WAS 1:1.2 FOR CRYOPROTECTION THE CONCENTRATION OF PEG 400 WAS ADJUSTED TO 36% V/V

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 101.6 α = 90
b = 113.04 β = 90
c = 74.5 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS V MIRRORS 2001-10-12
Diffraction Radiation
Monochromator Protocol
DIAMOND SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL45XU -- SPRING-8 BL45XU

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
2.08 30 99.4 0.069 -- -- 6.088 -- 25871 -- 0.0 44.0
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)
2.08 2.12 97.3 0.468 -- 3.13 4.55 --

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
OTHER 2.1 29.74 -- 0.0 -- 25194 1228 99.2 -- 0.229 0.229 0.277 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 2.1 2.23 -- 214 3848 0.27 0.333 0.023 97.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 48.3
Anisotropic B[1][1] 4.88
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.32
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.57
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 9.73
c_scbond_it 7.35
c_mcangle_it 6.25
c_mcbond_it 5.23
c_improper_angle_d 1.05
c_bond_d 0.005
c_angle_deg 0.9
c_dihedral_angle_d 14.7
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.29
Luzzati Sigma A (Observed) 0.21
Luzzati Resolution Cutoff (Low) 30.0
Luzzati ESD (R-Free Set) 0.35
Luzzati Sigma A (R-Free Set) 0.26
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1129
Nucleic Acid Atoms 650
Heterogen Atoms 0
Solvent Atoms 224

Software

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