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 CRYSTAL OF THE C-TERMINAL 31-KD DOMAIN OF RAT DNA POL BETA (SEE ENTRY 1BPB AND REFERENCE 9) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 1 MONTH: PEG 1500, 15% HEPES, 75 MILLIMOLAR, PH 7.5 NACL, 50 MILLIMOLAR DTT, 0.1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE., pH 6.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 120.18 α = 90
b = 62.88 β = 90
c = 38.29 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 XUONG-HAMLIN MULTIWIRE -- 1994-06-17
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH2R -- -- --

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
3 20 97.0 -- 0.064 -- 2.7 -- 6027 -- 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)
3.0 3.1 92.0 -- 0.166 1.9 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 3.0 20.0 -- 0.0 -- 6027 -- 97.0 -- -- -- -- --
RMS Deviations
Key Refinement Restraint Deviation
t_incorr_chiral_ct 0.0
t_bond_d 0.016
t_trig_c_planes 0.016
t_dihedral_angle_d 22.6
t_angle_deg 2.7
t_gen_planes 0.008
t_it 5.8
t_nbd 0.023
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1928
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 106

Software

Software
Software Name Purpose
TNT refinement version: 5-D
SDMS data reduction
SDMS data scaling
TNT phasing version: V. 5-D