X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Batch Under Oil
pH 7.5
Temperature 287.15
Details 3.5 micro L of protein solution (13.9 mg/ml protein in 200mM NaCl, 5% (v/v) glycerol, 2mM DTT, 0.025% (w/v) NaN3, 20mM HEPES buffer, pH 7.5) with 2.0 micro L of precipitant solution (50mM NH4Br, 50mM KC2H3O2, 100mM HEPES, pH 7.5 and 20%(w/v) PEG 20K, Batch under oil, temperature 287.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 176.61 α = 90
b = 176.61 β = 90
c = 72.19 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2008-04-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 1.1696 SSRL BL11-1

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
2.15 76.47 99.86 0.068 -- -- 11.2 -- 70276 -- 3.0 33.55
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)
2.15 2.27 99.5 0.348 -- 3.0 4.5 --

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
MRSAD 2.15 52.495 -- 1.33 70197 70196 3541 99.76 -- 0.1611 0.1603 0.1756 --
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 2.15 2.1794 -- 140 2650 0.2259 0.2858 -- 100.0
X Ray Diffraction 2.1794 2.2106 -- 140 2646 0.2244 0.224 -- 100.0
X Ray Diffraction 2.2106 2.2436 -- 120 2646 0.2199 0.2102 -- 99.0
X Ray Diffraction 2.2436 2.2786 -- 120 2641 0.2166 0.2458 -- 99.0
X Ray Diffraction 2.2786 2.316 -- 123 2670 0.2164 0.258 -- 100.0
X Ray Diffraction 2.316 2.3559 -- 139 2643 0.1978 0.1909 -- 100.0
X Ray Diffraction 2.3559 2.3988 -- 144 2647 0.1897 0.2003 -- 100.0
X Ray Diffraction 2.3988 2.4449 -- 131 2620 0.1901 0.2191 -- 100.0
X Ray Diffraction 2.4449 2.4948 -- 139 2682 0.1934 0.2375 -- 100.0
X Ray Diffraction 2.4948 2.5491 -- 147 2623 0.1792 0.2393 -- 100.0
X Ray Diffraction 2.5491 2.6084 -- 151 2639 0.1752 0.2076 -- 100.0
X Ray Diffraction 2.6084 2.6736 -- 132 2680 0.1707 0.2255 -- 100.0
X Ray Diffraction 2.6736 2.7459 -- 152 2646 0.1745 0.2003 -- 100.0
X Ray Diffraction 2.7459 2.8267 -- 167 2623 0.1724 0.1828 -- 100.0
X Ray Diffraction 2.8267 2.9179 -- 138 2682 0.1736 0.2319 -- 100.0
X Ray Diffraction 2.9179 3.0222 -- 142 2665 0.1828 0.2059 -- 99.0
X Ray Diffraction 3.0222 3.1432 -- 143 2653 0.1753 0.2081 -- 99.0
X Ray Diffraction 3.1432 3.2862 -- 159 2658 0.1673 0.1982 -- 100.0
X Ray Diffraction 3.2862 3.4594 -- 131 2678 0.161 0.1867 -- 100.0
X Ray Diffraction 3.4594 3.6761 -- 143 2677 0.1474 0.157 -- 100.0
X Ray Diffraction 3.6761 3.9598 -- 146 2670 0.1394 0.1481 -- 100.0
X Ray Diffraction 3.9598 4.3582 -- 151 2674 0.119 0.1291 -- 100.0
X Ray Diffraction 4.3582 4.9884 -- 148 2716 0.1171 0.1164 -- 100.0
X Ray Diffraction 4.9884 6.2832 -- 152 2717 0.1466 0.1538 -- 100.0
X Ray Diffraction 6.2832 52.5105 -- 143 2809 0.1586 0.148 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.045
f_dihedral_angle_d 13.584
f_angle_d 0.714
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4790
Nucleic Acid Atoms 0
Heterogen Atoms 75
Solvent Atoms 447

Software

Computing
Computing Package Purpose
BluIce Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: dev_1096) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: dev_1096) refinement
PHENIX model building
BluIce data collection