X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 277.0
Details 0.1M Magnesium formate dehydrate, 15%(w/v) Polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.35 α = 90
b = 171.78 β = 90
c = 117.44 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-04-20
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.97939 SSRF BL17U

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
3.1 50 99.9 0.076 0.076 -- 6.9 15515 15494 0.0 -3.0 --
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)
3.1 3.21 100.0 0.548 0.548 3.522 7.0 1525

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 3.1001 37.129 -- 1.35 -- 15471 774 99.9 -- 0.2613 0.2604 0.2778 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 3.1001 3.2942 -- 137 2413 0.3196 0.3211 -- 100.0
X Ray Diffraction 3.2942 3.5484 -- 134 2402 0.2967 0.3121 -- 100.0
X Ray Diffraction 3.5484 3.9051 -- 133 2409 0.2789 0.3335 -- 100.0
X Ray Diffraction 3.9051 4.4694 -- 123 2439 0.2445 0.2545 -- 100.0
X Ray Diffraction 4.4694 5.6278 -- 109 2492 0.2194 0.2621 -- 100.0
X Ray Diffraction 5.6278 37.1316 -- 138 2542 0.2634 0.2531 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -1.2708
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.2376
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0332
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.079
f_dihedral_angle_d 19.454
f_angle_d 1.08
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4927
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 79

Software

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