X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 292.0
Details 0.02M CACL2, 0.1 NA ACETATE, 30% MPD, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.4 α = 90
b = 43.4 β = 90
c = 143.12 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal 2011-10-14
Diffraction Radiation
Monochromator Protocol
CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.980 SOLEIL PROXIMA 1

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
1.16 41.53 99.5 0.08 -- -- 5.08 -- 48400 1.35 -- 14.97
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)
1.16 1.23 97.8 -- -- -- -- --

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 1.16 32.103 -- 1.35 48528 48392 4840 99.72 -- 0.1254 0.1228 0.1493 --
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 1.1601 1.1733 -- 157 1408 0.2124 0.2557 -- 98.0
X Ray Diffraction 1.1733 1.1871 -- 155 1401 0.1736 0.2167 -- 99.0
X Ray Diffraction 1.1871 1.2015 -- 159 1425 0.1635 0.2006 -- 99.0
X Ray Diffraction 1.2015 1.2168 -- 156 1408 0.1619 0.1744 -- 100.0
X Ray Diffraction 1.2168 1.2328 -- 159 1426 0.1508 0.2053 -- 100.0
X Ray Diffraction 1.2328 1.2497 -- 159 1433 0.1457 0.205 -- 100.0
X Ray Diffraction 1.2497 1.2675 -- 157 1417 0.1383 0.1872 -- 100.0
X Ray Diffraction 1.2675 1.2864 -- 160 1436 0.1407 0.1894 -- 100.0
X Ray Diffraction 1.2864 1.3065 -- 159 1429 0.1339 0.1853 -- 100.0
X Ray Diffraction 1.3065 1.328 -- 159 1439 0.1208 0.1673 -- 100.0
X Ray Diffraction 1.328 1.3509 -- 159 1427 0.111 0.1599 -- 100.0
X Ray Diffraction 1.3509 1.3754 -- 158 1417 0.1127 0.1482 -- 100.0
X Ray Diffraction 1.3754 1.4019 -- 161 1457 0.1104 0.1482 -- 100.0
X Ray Diffraction 1.4019 1.4305 -- 159 1434 0.0996 0.1541 -- 100.0
X Ray Diffraction 1.4305 1.4616 -- 161 1443 0.0964 0.145 -- 100.0
X Ray Diffraction 1.4616 1.4956 -- 162 1464 0.0968 0.1422 -- 100.0
X Ray Diffraction 1.4956 1.533 -- 158 1418 0.0902 0.1344 -- 100.0
X Ray Diffraction 1.533 1.5744 -- 160 1441 0.0884 0.1356 -- 100.0
X Ray Diffraction 1.5744 1.6208 -- 161 1452 0.0995 0.1208 -- 100.0
X Ray Diffraction 1.6208 1.6731 -- 163 1458 0.0975 0.1343 -- 100.0
X Ray Diffraction 1.6731 1.7329 -- 161 1447 0.1023 0.1272 -- 100.0
X Ray Diffraction 1.7329 1.8022 -- 162 1467 0.1015 0.1271 -- 100.0
X Ray Diffraction 1.8022 1.8843 -- 161 1441 0.1013 0.1145 -- 100.0
X Ray Diffraction 1.8843 1.9836 -- 163 1471 0.1102 0.1408 -- 100.0
X Ray Diffraction 1.9836 2.1078 -- 163 1470 0.1039 0.1207 -- 100.0
X Ray Diffraction 2.1078 2.2706 -- 164 1479 0.1103 0.128 -- 100.0
X Ray Diffraction 2.2706 2.499 -- 165 1475 0.1082 0.1315 -- 99.0
X Ray Diffraction 2.499 2.8604 -- 167 1501 0.1192 0.1328 -- 100.0
X Ray Diffraction 2.8604 3.603 -- 171 1544 0.1294 0.1564 -- 100.0
X Ray Diffraction 3.603 32.1155 -- 181 1624 0.1649 0.1775 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.3291
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.3291
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.6581
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.083
f_dihedral_angle_d 13.824
f_angle_d 1.8
f_bond_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1232
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 167

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHASER model building