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-BROMOTHIENYLDEOXYURIDINE 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-BROMOTHIENYLDEOXYURIDINE (BTDU)., vapor diffusion - hanging drop

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 114.1 α = 90
b = 116 β = 90
c = 108.7 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 1996-08
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
2.34 -- 100.0 -- 0.144 -- 4.0 -- 29537 -- -3.0 24.07
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)
2.34 2.52 100.0 -- -- 4.5 4.0 --

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 2.34 12.0 -- 1.2 -- 25327 2515 83.0 -- 0.21 0.21 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 2.34 2.42 -- 214 1742 0.275 0.344 -- 65.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model INDIVIDUAL B-FACTOR REFT.
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 2.0
x_scbond_it 1.5
x_mcangle_it 2.0
x_mcbond_it 1.5
x_improper_angle_d 1.616
x_bond_d 0.013
x_angle_deg 2.016
x_dihedral_angle_d 22.77
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4625
Nucleic Acid Atoms 0
Heterogen Atoms 54
Solvent Atoms 263

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
RAVE, SOLOMON Structure Solution
X-PLOR 3.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.1 refinement
SOLOMON model building
RAVE model building