X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.8
Temperature 277.0
Details 0.1M magnesium acetate, 50mM 2-(N-morpholino)ethanesulfonic acid pH 5.8, 22% 2-methyl-2, 4-pentanediol (MPT), VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.15 α = 90
b = 176.8 β = 111.58
c = 94.07 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2010-12-02
Diffraction Radiation
Monochromator Protocol
Fixed-Exit Double Crystal Monochromator (Crystal type Si(1 1 1)) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL12B2 0.90000 SPRING-8 BL12B2

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
2.16 30 95.7 -- 0.06 -- 2.6 123847 129411 1.0 1.0 32.09
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)
2.16 2.2 98.2 0.472 0.472 2.1 2.3 --

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 2.162 29.543 -- 0.0 129619 117720 5917 90.82 -- 0.1701 0.1682 0.2072 --
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 2.1619 2.2391 -- 572 10113 0.2325 0.2882 -- 82.0
X Ray Diffraction 2.2391 2.3288 -- 537 10652 0.2097 0.2689 -- 87.0
X Ray Diffraction 2.3288 2.4347 -- 576 11012 0.1945 0.2482 -- 90.0
X Ray Diffraction 2.4347 2.563 -- 576 11223 0.1902 0.2316 -- 91.0
X Ray Diffraction 2.563 2.7235 -- 574 11420 0.1781 0.2357 -- 93.0
X Ray Diffraction 2.7235 2.9336 -- 630 11577 0.1712 0.2131 -- 94.0
X Ray Diffraction 2.9336 3.2285 -- 652 11605 0.1656 0.2181 -- 95.0
X Ray Diffraction 3.2285 3.6949 -- 594 11700 0.1513 0.1895 -- 95.0
X Ray Diffraction 3.6949 4.6522 -- 625 11317 0.1397 0.1686 -- 92.0
X Ray Diffraction 4.6522 29.5462 -- 581 11184 0.1726 0.1982 -- 90.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.0272
Anisotropic B[1][1] 6.3155
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 5.9953
Anisotropic B[2][2] 1.0717
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.9119
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.069
f_dihedral_angle_d 15.442
f_angle_d 1.058
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10826
Nucleic Acid Atoms 820
Heterogen Atoms 90
Solvent Atoms 1047

Software

Computing
Computing Package Purpose
bluice Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX (phenix.automr: 1.6.4_486) Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.4_486) refinement
PHENIX version: (phenix.automr: 1.6.4_486) model building
bluice data collection