X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 277.0
Details 0.1 M sodium acetate, pH 4.5, 30% (w/v) PEG-6000, 0.3 M LiSO4, 3% (w/v) TMAO, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide, vapor diffusion, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.06 α = 90
b = 75.81 β = 93.11
c = 52.71 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 315r -- 2012-06-02
Diffraction Radiation
Monochromator Protocol
two flat Si(111) crystals, mounted in a model DCM from Khozu SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.116 ALS 8.3.1

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
1.55 47.99 95.7 0.052 -- -- -- -- 52337 -- -3.0 21.494
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)
1.55 1.63 92.3 0.367 -- 3.07 -- --

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 1.55 47.989 -- 1.99 -- 52336 2103 95.66 -- 0.1757 0.1747 0.1985 RANDOM
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 1.55 1.5861 -- 132 2962 0.284 0.2566 -- 86.0
X Ray Diffraction 1.5861 1.6257 -- 137 3410 0.2595 0.3008 -- 97.0
X Ray Diffraction 1.6257 1.6697 -- 143 3460 0.2361 0.2706 -- 99.0
X Ray Diffraction 1.6697 1.7188 -- 144 3453 0.2115 0.2564 -- 99.0
X Ray Diffraction 1.7188 1.7743 -- 149 3457 0.1933 0.2211 -- 99.0
X Ray Diffraction 1.7743 1.8377 -- 137 3413 0.1746 0.2076 -- 99.0
X Ray Diffraction 1.8377 1.9113 -- 146 3436 0.1663 0.1976 -- 98.0
X Ray Diffraction 1.9113 1.9983 -- 140 3422 0.1615 0.1895 -- 98.0
X Ray Diffraction 1.9983 2.1036 -- 139 3437 0.1643 0.2052 -- 98.0
X Ray Diffraction 2.1036 2.2354 -- 144 3391 0.1617 0.19 -- 97.0
X Ray Diffraction 2.2354 2.408 -- 144 3360 0.1587 0.1973 -- 96.0
X Ray Diffraction 2.408 2.6503 -- 142 3354 0.1613 0.2138 -- 95.0
X Ray Diffraction 2.6503 3.0338 -- 138 3287 0.171 0.1897 -- 94.0
X Ray Diffraction 3.0338 3.822 -- 137 3227 0.1598 0.1621 -- 92.0
X Ray Diffraction 3.822 48.0123 -- 131 3164 0.1705 0.176 -- 88.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.6634
Anisotropic B[1][1] -1.6965
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.3838
Anisotropic B[2][2] 1.7092
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.0127
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.481
f_plane_restr 0.011
f_chiral_restr 0.142
f_angle_d 1.941
f_bond_d 0.021
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2743
Nucleic Acid Atoms 0
Heterogen Atoms 77
Solvent Atoms 320

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
XSCALE Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction