X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 277.0
Details 0.07M Sodium Iodide, 30.00% polyethylene glycol 3350, 0.01M ferric(III) chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.14 α = 90
b = 37.11 β = 121.66
c = 61.38 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
PIXEL DECTRIS PILATUS 6M FLAT MIRROR (VERTICAL FOCUSING), SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING) 2013-11-25
Diffraction Radiation
Monochromator Protocol
SINGLE CRYSTAL SI(111) BENT SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
-- -- -- -- --
SYNCHROTRON SSRL BEAMLINE BL11-1 -- SSRL BL11-1

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
1.27 28 97.0 -- -- -- -- -- 53919 -- -3.0 14.53
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)
1.27 1.32 97.7 0.385 -- 2.6 -- --

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
SAD 1.27 28.0 -- -- -- 53907 2753 98.1 -- 0.155 0.154 0.176 --
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 1.27 1.2919 -- 145 2514 0.1547 0.1966 -- 98.0
X Ray Diffraction 1.2919 1.3154 -- 131 2578 0.1416 0.2037 -- 99.0
X Ray Diffraction 1.3154 1.3407 -- 131 2506 0.1329 0.1839 -- 98.0
X Ray Diffraction 1.3407 1.3681 -- 149 2558 0.1276 0.1633 -- 98.0
X Ray Diffraction 1.3681 1.3978 -- 131 2560 0.1214 0.1528 -- 99.0
X Ray Diffraction 1.3978 1.4303 -- 119 2585 0.1147 0.1821 -- 98.0
X Ray Diffraction 1.4303 1.4661 -- 129 2587 0.1142 0.1803 -- 99.0
X Ray Diffraction 1.4661 1.5057 -- 151 2552 0.1039 0.1472 -- 99.0
X Ray Diffraction 1.5057 1.55 -- 124 2543 0.102 0.1295 -- 98.0
X Ray Diffraction 1.55 1.6 -- 138 2515 0.1049 0.1483 -- 98.0
X Ray Diffraction 1.6 1.6572 -- 149 2579 0.1102 0.1528 -- 99.0
X Ray Diffraction 1.6572 1.7236 -- 141 2574 0.115 0.1528 -- 99.0
X Ray Diffraction 1.7236 1.802 -- 165 2571 0.1236 0.1809 -- 99.0
X Ray Diffraction 1.802 1.897 -- 154 2542 0.1276 0.15 -- 99.0
X Ray Diffraction 1.897 2.0158 -- 130 2487 0.1278 0.1759 -- 96.0
X Ray Diffraction 2.0158 2.1714 -- 129 2622 0.1348 0.1636 -- 99.0
X Ray Diffraction 2.1714 2.3898 -- 164 2556 0.1478 0.1685 -- 99.0
X Ray Diffraction 2.3898 2.7353 -- 121 2552 0.1616 0.1867 -- 96.0
X Ray Diffraction 2.7353 3.445 -- 131 2534 0.1768 0.1952 -- 96.0
X Ray Diffraction 3.445 26.9079 -- 121 2639 0.2033 0.1883 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.42
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.725
f_plane_restr 0.01
f_bond_d 0.011
f_dihedral_angle_d 18.421
f_chiral_restr 0.079
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1704
Nucleic Acid Atoms 0
Heterogen Atoms 82
Solvent Atoms 184

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
XSCALE data scaling
PHENIX refinement version: 1.8.4
XDS data reduction
SHELXD phasing