X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details PEG6000, HEPES

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.86 α = 90
b = 108.86 β = 90
c = 182.38 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 MONOCHROMATOR; MIRROR 2009-04-11
CCD ADSC QUANTUM 315 MIRROR 2009-02-09
Diffraction Radiation
Monochromator Protocol
CRYSTAL SI(111) BENT MONOCHROMATOR SINGLE WAVELENGTH
LN2-COOLED DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSRRC BEAMLINE BL13C1 1.0 NSRRC BL13C1
SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1

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
2.88 30 99.7 0.081 -- 25.328 6.8 -- 25404 -- -- 38.94
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)
2.88 2.98 100.0 0.252 -- -- 7.1 2715

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 2.884 26.475 -- 1.34 -- 25330 1998 99.73 -- 0.1659 0.1636 0.1929 --
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 2.884 2.956 -- 140 1641 0.2172 0.2502 -- 100.0
X Ray Diffraction 2.956 3.0358 -- 140 1626 0.2245 0.2674 -- 100.0
X Ray Diffraction 3.0358 3.125 -- 141 1644 0.2235 0.2505 -- 100.0
X Ray Diffraction 3.125 3.2257 -- 141 1646 0.2097 0.2464 -- 100.0
X Ray Diffraction 3.2257 3.3408 -- 140 1632 0.2 0.2333 -- 100.0
X Ray Diffraction 3.3408 3.4743 -- 139 1636 0.1967 0.2432 -- 100.0
X Ray Diffraction 3.4743 3.632 -- 143 1666 0.174 0.2311 -- 100.0
X Ray Diffraction 3.632 3.823 -- 140 1641 0.1654 0.1888 -- 100.0
X Ray Diffraction 3.823 4.0617 -- 144 1675 0.1369 0.1756 -- 100.0
X Ray Diffraction 4.0617 4.374 -- 140 1656 0.1358 0.1363 -- 100.0
X Ray Diffraction 4.374 4.8118 -- 145 1679 0.1237 0.1678 -- 100.0
X Ray Diffraction 4.8118 5.5026 -- 144 1687 0.135 0.1535 -- 100.0
X Ray Diffraction 5.5026 6.9123 -- 147 1711 0.1409 0.1623 -- 100.0
X Ray Diffraction 6.9123 26.4757 -- 154 1792 0.1509 0.1681 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.1304
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.592
f_angle_d 1.107
f_plane_restr 0.007
f_bond_d 0.006
f_chiral_restr 0.049
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5012
Nucleic Acid Atoms 0
Heterogen Atoms 81
Solvent Atoms 27

Software

Software
Software Name Purpose
SCALEPACK data reduction
PHASER phasing version: 2.5.3
RESOLVE phasing version: 2.15
PHENIX refinement version: (phenix.refine: 1.9_1692)
PDB_EXTRACT data extraction version: 3.15