X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Details HANGING-DROP: 8ML PROTEIN SOLUTION PLUS 4ML PRECIPITATING SOLUTION EQUILIBRATED AGAINST PRECIPITATING SOLUTION AT 25 C. PROTEIN SOLUTION: HSV-TK 1.0MG/ML; 40MM TRIS-CL PH 7.5; 3MM DTT; 0.2MM DT. PRECIPITATING SOLUTION: 30% SATURATED AMMONIUM SULPHATE; 200MM TRIS-CL PH 6.75; 3MM DTT; 0.2 MM DT. EXCHANGE OF DEOXYTHYMIDINE BOUND TO THE PROTEIN FOR 5-BROMOVINYLDEOXYURIDINE WAS MADE BY WASHING THE CRYSTALS FIVE TIMES IN A 3 ML SOLUTION (33% SATURATED AMMONIUM SULPHATE; 100MM TRIS-CL PH 6.75) CONTAINING 5-BROMOVINYLDEOXYURIDINE (BVDU)., vapor diffusion - hanging drop

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 113.4 α = 90
b = 116.9 β = 90
c = 108.2 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC MIRRORS 1996-11
Diffraction Radiation
Monochromator Protocol
OTWINOWSKI MIRRORS --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
-- -- -- -- --

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
2.15 -- 95.0 -- 0.118 -- 4.0 -- 36243 -- -3.0 25.8
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)
2.15 2.25 92.0 -- -- 1.5 2.0 --

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
MIR + NCS IMPROVEMENT AND SOLVENT FLATTENING FOR ORIGINAL NATIVE, 1KIN 2.2 12.0 -- 2.8 -- 28510 2853 78.0 -- 0.199 0.199 0.29 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 2.2 2.28 -- 207 1917 0.287 0.346 -- 78.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model INDIVIDUAL B-FACTOR REFT.
Mean Isotropic B 19.0
RMS Deviations
Key Refinement Restraint Deviation
x_dihedral_angle_d 22.74
x_scbond_it 1.5
x_mcbond_it 1.5
x_scangle_it 2.0
x_improper_angle_d 1.724
x_bond_d 0.011
x_mcangle_it 2.0
x_angle_deg 1.921
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4676
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 249

Software

Software
Software Name Purpose
SOLOMON phasing
X-PLOR refinement version: 3.1
DENZO data reduction
SCALEPACK data scaling