X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 277.0
Details Mother liqueur contained 28% PEG 400, 100 mM HEPES, NaOH, 200 mM Calcium chloride. Protein solution was at 20 mg/mL, 100 mM NaCl, 50 mM Tris, pH 7.5, vapor diffusion, sitting drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 125.77 α = 90
b = 125.77 β = 90
c = 119.74 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-325 -- 2003-01-01
Diffraction Radiation
Monochromator Protocol
C(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G

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
1.25 29.9 100.0 0.093 -- -- -- 131226 131204 0.0 -3.0 15.263
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)
1.25 1.28 100.0 0.766 -- 3.84 -- --

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 1.25 29.9 -- 2.0 131204 131191 6560 99.98 -- 0.1413 0.141 0.1482 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 1.25 1.2642 -- 216 4117 0.1861 0.1965 -- 100.0
X Ray Diffraction 1.2642 1.2791 -- 216 4098 0.1821 0.1796 -- 100.0
X Ray Diffraction 1.2791 1.2947 -- 217 4131 0.1771 0.2041 -- 100.0
X Ray Diffraction 1.2947 1.311 -- 216 4095 0.1681 0.1713 -- 100.0
X Ray Diffraction 1.311 1.3283 -- 217 4121 0.1621 0.1678 -- 100.0
X Ray Diffraction 1.3283 1.3465 -- 217 4130 0.1603 0.1724 -- 100.0
X Ray Diffraction 1.3465 1.3657 -- 216 4104 0.1557 0.1598 -- 100.0
X Ray Diffraction 1.3657 1.3861 -- 216 4104 0.1566 0.1639 -- 100.0
X Ray Diffraction 1.3861 1.4078 -- 218 4124 0.1488 0.1582 -- 100.0
X Ray Diffraction 1.4078 1.4309 -- 217 4129 0.1475 0.1614 -- 100.0
X Ray Diffraction 1.4309 1.4555 -- 216 4099 0.141 0.1452 -- 100.0
X Ray Diffraction 1.4555 1.482 -- 218 4145 0.1371 0.1558 -- 100.0
X Ray Diffraction 1.482 1.5105 -- 217 4127 0.1336 0.1341 -- 100.0
X Ray Diffraction 1.5105 1.5413 -- 217 4120 0.1308 0.1484 -- 100.0
X Ray Diffraction 1.5413 1.5748 -- 218 4149 0.1318 0.1479 -- 100.0
X Ray Diffraction 1.5748 1.6115 -- 217 4110 0.129 0.1467 -- 100.0
X Ray Diffraction 1.6115 1.6518 -- 217 4136 0.1289 0.1449 -- 100.0
X Ray Diffraction 1.6518 1.6964 -- 219 4155 0.1275 0.1432 -- 100.0
X Ray Diffraction 1.6964 1.7463 -- 218 4144 0.132 0.1391 -- 100.0
X Ray Diffraction 1.7463 1.8027 -- 218 4133 0.1326 0.1475 -- 100.0
X Ray Diffraction 1.8027 1.8671 -- 218 4159 0.133 0.1431 -- 100.0
X Ray Diffraction 1.8671 1.9419 -- 220 4167 0.1347 0.1586 -- 100.0
X Ray Diffraction 1.9419 2.0302 -- 219 4170 0.1339 0.1546 -- 100.0
X Ray Diffraction 2.0302 2.1372 -- 220 4170 0.1363 0.1389 -- 100.0
X Ray Diffraction 2.1372 2.2711 -- 218 4149 0.1314 0.1512 -- 100.0
X Ray Diffraction 2.2711 2.4464 -- 222 4214 0.1397 0.1508 -- 100.0
X Ray Diffraction 2.4464 2.6924 -- 221 4191 0.1424 0.1436 -- 100.0
X Ray Diffraction 2.6924 3.0817 -- 222 4231 0.1448 0.1426 -- 100.0
X Ray Diffraction 3.0817 3.8813 -- 225 4264 0.1372 0.1389 -- 100.0
X Ray Diffraction 3.8813 29.9436 -- 234 4445 0.1456 0.1358 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.2156
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.55
f_plane_restr 0.006
f_chiral_restr 0.076
f_angle_d 1.138
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3072
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 534

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
Xscale data reduction