X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 3 DAYS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR CACL2, 0.1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 178.47 α = 90
b = 57.8 β = 90
c = 48.44 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR SDMS -- 1995-03-26
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
2.8 20 90.0 -- 0.046 -- 1.9 -- 11597 -- 0.0 --
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)
2.8 2.9 86.0 -- 0.145 -- 1.4 --

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
DIFFERENCE FOURIER 2.8 20.0 -- 0.0 -- 11597 -- 90.0 -- -- 0.162 -- --
RMS Deviations
Key Refinement Restraint Deviation
t_nbd 0.021
t_it 5.2
t_gen_planes 0.005
t_trig_c_planes 0.012
t_incorr_chiral_ct 0.0
t_dihedral_angle_d 23.9
t_angle_deg 2.9
t_bond_d 0.018
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2623
Nucleic Acid Atoms 248
Heterogen Atoms 2
Solvent Atoms 163

Software

Computing
Computing Package Purpose
SDMS Data Reduction (intensity integration)
SDMS Data Reduction (data scaling)
TNT V. 5-D Structure Solution
TNT V. 5-D Structure Refinement
Software
Software Name Purpose
TNT version: 5-D refinement
TNT version: 5-D model building
SDMS data reduction
SDMS data collection