X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 293.0
Details PEG 6000, citrate buffer, CdCl2, MPD, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 99.74 α = 90
b = 169.84 β = 90
c = 175.26 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE -- 2012-11-14
Diffraction Radiation
Monochromator Protocol
Si SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPRING-8 BL41XU

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
3.3 50 99.6 -- 0.141 -- 5.4 45965 45365 -- -1.0 --
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)
3.3 3.42 99.3 0.654 0.654 2.25 4.2 4570

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 3.3 41.765 -- 1.38 -- 45304 2329 99.48 -- 0.2523 0.2503 0.2893 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 3.2989 3.3662 -- 121 2432 0.3775 0.3899 -- 97.0
X Ray Diffraction 3.3662 3.4394 -- 131 2511 0.3547 0.3628 -- 100.0
X Ray Diffraction 3.4394 3.5194 -- 147 2455 0.3544 0.3593 -- 100.0
X Ray Diffraction 3.5194 3.6073 -- 138 2488 0.3325 0.3331 -- 99.0
X Ray Diffraction 3.6073 3.7048 -- 144 2507 0.3203 0.3822 -- 99.0
X Ray Diffraction 3.7048 3.8137 -- 118 2510 0.2981 0.3287 -- 100.0
X Ray Diffraction 3.8137 3.9368 -- 140 2516 0.2845 0.331 -- 100.0
X Ray Diffraction 3.9368 4.0773 -- 134 2480 0.2703 0.2933 -- 100.0
X Ray Diffraction 4.0773 4.2404 -- 146 2494 0.2466 0.3323 -- 100.0
X Ray Diffraction 4.2404 4.4332 -- 140 2516 0.2406 0.2977 -- 100.0
X Ray Diffraction 4.4332 4.6667 -- 132 2523 0.2243 0.2405 -- 100.0
X Ray Diffraction 4.6667 4.9586 -- 115 2569 0.2065 0.2464 -- 100.0
X Ray Diffraction 4.9586 5.3408 -- 143 2546 0.219 0.2676 -- 100.0
X Ray Diffraction 5.3408 5.8769 -- 149 2551 0.2364 0.2637 -- 100.0
X Ray Diffraction 5.8769 6.7243 -- 150 2563 0.2495 0.2668 -- 100.0
X Ray Diffraction 6.7243 8.4603 -- 137 2605 0.2167 0.2726 -- 100.0
X Ray Diffraction 8.4603 41.7678 -- 144 2709 0.1821 0.2298 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 96.88
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.015
f_chiral_restr 0.035
f_dihedral_angle_d 15.879
f_angle_d 0.886
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14421
Nucleic Acid Atoms 1609
Heterogen Atoms 59
Solvent Atoms 7

Software

Computing
Computing Package Purpose
PHENIX (phenix.refine: 1.8.4_1496) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.4_1496) refinement