X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 277.15
Details 15% PEG 8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.9 α = 90
b = 71.1 β = 100.6
c = 72.9 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 Collimating mirror 2009-12-12
Diffraction Radiation
Monochromator Protocol
Double Crystal Monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2

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
1.78 50 97.9 -- 0.078 -- 3.0 32972 32972 -- -- 13.54
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)
1.78 1.81 99.4 -- 0.476 2.1 2.9 1610

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 1.78 34.354 -- 0.0 32760 31209 1551 92.76 0.1559 0.1559 0.1544 0.1852 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 1.78 1.8436 -- 150 2692 0.2066 0.2814 -- 85.0
X Ray Diffraction 1.8436 1.9174 -- 156 2764 0.1854 0.2398 -- 87.0
X Ray Diffraction 1.9174 2.0047 -- 151 2898 0.1595 0.2017 -- 91.0
X Ray Diffraction 2.0047 2.1104 -- 154 3001 0.1508 0.2078 -- 94.0
X Ray Diffraction 2.1104 2.2426 -- 155 3013 0.1386 0.1561 -- 94.0
X Ray Diffraction 2.2426 2.4157 -- 167 3020 0.1386 0.1768 -- 95.0
X Ray Diffraction 2.4157 2.6587 -- 140 3054 0.1595 0.1769 -- 95.0
X Ray Diffraction 2.6587 3.0432 -- 155 3064 0.1659 0.2368 -- 95.0
X Ray Diffraction 3.0432 3.8333 -- 168 3091 0.1449 0.1694 -- 96.0
X Ray Diffraction 3.8333 34.36 -- 155 3061 0.149 0.1488 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.3951
Anisotropic B[1][1] 3.9133
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -4.2516
Anisotropic B[2][2] -2.1641
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.7492
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.28
f_plane_restr 0.005
f_chiral_restr 0.074
f_angle_d 1.055
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2341
Nucleic Acid Atoms 0
Heterogen Atoms 68
Solvent Atoms 314

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.4_486) refinement
PHASER model building
MAR345dtb data collection