X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch Under Oil
pH 6
Temperature 288.0
Details Equal volumes of precipitant, protein solution and DNA. Precipitant: sodium malonate Crystal Screen C4- 2.4 M sodium malonate pH 6.0. Protein: 20 mM Tris base (pH 8.0), 0.5 M NaCl, 10% glycerol, 150 mM imidazole, 10 mM BME, MICROBATCH UNDER OIL, temperature 288K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 156.49 α = 90
b = 156.49 β = 90
c = 141.52 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2008-07-23
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 0.99999 APS 22-BM

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
3.1 200 92.7 0.114 -- -- 8.2 -- 30569 -- -- 99.4
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)
3.1 3.21 72.5 0.399 -- -- 3.0 2350

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
MOLECULAR REPLACEMENT 3.1 48.95 -- 0.0 -- 30320 1523 91.97 -- 0.1794 0.1782 0.2029 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 3.1 3.165 -- 68 1481 0.25 0.294 -- 67.406
X Ray Diffraction 3.165 3.252 -- 102 1607 0.215 0.256 -- 78.215
X Ray Diffraction 3.252 3.346 -- 114 1662 0.229 0.263 -- 84.451
X Ray Diffraction 3.346 3.449 -- 80 1802 0.228 0.254 -- 91.715
X Ray Diffraction 3.449 3.562 -- 94 1753 0.206 0.241 -- 94.283
X Ray Diffraction 3.562 3.687 -- 93 1695 0.196 0.239 -- 94.904
X Ray Diffraction 3.687 3.826 -- 70 1686 0.189 0.181 -- 95.591
X Ray Diffraction 3.826 3.982 -- 85 1620 0.181 0.25 -- 96.765
X Ray Diffraction 3.982 4.159 -- 78 1532 0.166 0.223 -- 96.234
X Ray Diffraction 4.159 4.361 -- 82 1465 0.141 0.197 -- 97.418
X Ray Diffraction 4.361 4.597 -- 75 1401 0.132 0.143 -- 96.534
X Ray Diffraction 4.597 4.875 -- 77 1290 0.149 0.161 -- 96.471
X Ray Diffraction 4.875 5.211 -- 64 1236 0.175 0.177 -- 96.654
X Ray Diffraction 5.211 5.628 -- 57 1139 0.19 0.209 -- 96.374
X Ray Diffraction 5.628 6.163 -- 49 1045 0.222 0.283 -- 95.713
X Ray Diffraction 6.163 6.888 -- 50 929 0.182 0.206 -- 96.169
X Ray Diffraction 6.888 7.949 -- 38 816 0.135 0.175 -- 94.784
X Ray Diffraction 7.949 9.722 -- 47 658 0.141 0.149 -- 94.504
X Ray Diffraction 9.722 13.697 -- 16 503 0.162 0.155 -- 92.844
X Ray Diffraction 13.697 110.657 -- 6 244 0.276 0.291 -- 82.508
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 108.173
Anisotropic B[1][1] 0.85
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.85
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.7
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.005
r_chiral_restr 0.062
r_dihedral_angle_4_deg 14.37
r_dihedral_angle_3_deg 17.221
r_dihedral_angle_2_deg 35.28
r_dihedral_angle_1_deg 5.336
r_angle_other_deg 0.843
r_angle_refined_deg 0.994
r_bond_other_d 0.001
r_bond_refined_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2922
Nucleic Acid Atoms 2038
Heterogen Atoms 15
Solvent Atoms 20

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Molecular Replacement Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: refmac_5.6.0117 refinement
SCALEPACK data reduction
DENZO data collection