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 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 179.61 α = 90
b = 57.63 β = 90
c = 48.28 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 -- 1995-02-06
Diffraction Radiation
Monochromator Protocol
GRAPHITE --
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
2.9 20 84.0 -- 0.049 -- 1.8 -- 9877 -- 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)
2.9 3.0 72.0 -- 0.152 -- 1.5 --

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 2.9 20.0 -- 0.0 -- 9877 -- 84.0 -- 0.166 -- -- --
RMS Deviations
Key Refinement Restraint Deviation
t_nbd 0.029
t_it 5.7
t_gen_planes 0.006
t_trig_c_planes 0.015
t_incorr_chiral_ct 0.0
t_dihedral_angle_d 19.0
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 310
Heterogen Atoms 13
Solvent Atoms 139

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