X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 293.0
Details 0.2M Magnesium acetate, 0.2M Sodium Acetate buffer (pH 6.0), 20%(w/v) PEG 6000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.36 α = 96.7
b = 80.28 β = 102.3
c = 127.74 γ = 112.1
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE -- 2017-07-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.00 SPring-8 BL26B1

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
1.3 50 94.4 0.052 -- 0.201 3.8 -- 495665 -- -- 15.0
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)
1.3 1.34 88.0 0.334 -- 3.5 2.7 --

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 1.297 39.264 -- 1.97 -- 495634 24855 94.41 -- 0.1291 0.1278 0.1537 --
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 1.297 1.3118 -- 746 13599 0.1838 0.2223 -- 82.0
X Ray Diffraction 1.3118 1.3272 -- 795 15042 0.1761 0.2121 -- 91.0
X Ray Diffraction 1.3272 1.3434 -- 793 15274 0.1712 0.2123 -- 91.0
X Ray Diffraction 1.3434 1.3604 -- 803 15223 0.1747 0.2103 -- 91.0
X Ray Diffraction 1.3604 1.3783 -- 768 15193 0.1645 0.1953 -- 91.0
X Ray Diffraction 1.3783 1.3972 -- 776 15222 0.1582 0.2023 -- 92.0
X Ray Diffraction 1.3972 1.4171 -- 876 15261 0.1557 0.1946 -- 92.0
X Ray Diffraction 1.4171 1.4383 -- 780 15441 0.1493 0.1957 -- 92.0
X Ray Diffraction 1.4383 1.4608 -- 828 15320 0.138 0.1753 -- 92.0
X Ray Diffraction 1.4608 1.4847 -- 829 15524 0.1342 0.1692 -- 93.0
X Ray Diffraction 1.4847 1.5103 -- 820 15473 0.129 0.1733 -- 93.0
X Ray Diffraction 1.5103 1.5378 -- 831 15495 0.1287 0.162 -- 94.0
X Ray Diffraction 1.5378 1.5674 -- 854 15580 0.1262 0.1676 -- 94.0
X Ray Diffraction 1.5674 1.5994 -- 866 15670 0.1239 0.1715 -- 94.0
X Ray Diffraction 1.5994 1.6341 -- 863 15774 0.1205 0.1561 -- 95.0
X Ray Diffraction 1.6341 1.6721 -- 828 15806 0.1245 0.1667 -- 95.0
X Ray Diffraction 1.6721 1.714 -- 858 15726 0.1224 0.1626 -- 95.0
X Ray Diffraction 1.714 1.7603 -- 851 15882 0.1248 0.1576 -- 96.0
X Ray Diffraction 1.7603 1.8121 -- 861 15917 0.1279 0.1639 -- 96.0
X Ray Diffraction 1.8121 1.8706 -- 831 15986 0.1282 0.1579 -- 96.0
X Ray Diffraction 1.8706 1.9375 -- 859 15969 0.1283 0.1583 -- 96.0
X Ray Diffraction 1.9375 2.015 -- 841 16129 0.1257 0.1455 -- 97.0
X Ray Diffraction 2.015 2.1067 -- 783 16155 0.1255 0.1426 -- 97.0
X Ray Diffraction 2.1067 2.2178 -- 803 16202 0.1209 0.1419 -- 97.0
X Ray Diffraction 2.2178 2.3567 -- 841 16191 0.1258 0.1489 -- 98.0
X Ray Diffraction 2.3567 2.5387 -- 865 16245 0.1256 0.1437 -- 98.0
X Ray Diffraction 2.5387 2.7941 -- 851 16299 0.1321 0.1601 -- 98.0
X Ray Diffraction 2.7941 3.1982 -- 847 16426 0.132 0.1571 -- 99.0
X Ray Diffraction 3.1982 4.0288 -- 877 16444 0.1168 0.1413 -- 99.0
X Ray Diffraction 4.0288 39.264 -- 831 16311 0.1219 0.1321 -- 98.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.965
f_dihedral_angle_d 21.824
f_chiral_restr 0.088
f_bond_d 0.009
f_plane_restr 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 16050
Nucleic Acid Atoms 0
Heterogen Atoms 55
Solvent Atoms 3132

Software

Software
Software Name Purpose
PHENIX refinement version: (1.10.1_2155: ???)
DENZO data reduction
SCALA data scaling
MOLREP phasing
HKL-2000 data collection