X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.9
Temperature 277.15
Details 2.2 M sodium/potassium phosphate, pH 6.9, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.23 α = 90
b = 60.23 β = 90
c = 96.87 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2015-06-03
Diffraction Radiation
Monochromator Protocol
KHOZU Double flat crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.11587 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
1.41 45.93 99.6 0.058 -- -- 8.0 -- 39667 -- -- --
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)
1.41 1.46 99.6 0.321 -- -- -- --

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 1.41 45.926 -- 1.35 -- 39665 1997 99.49 -- 0.2213 0.2201 0.2429 --
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 1.41 1.4452 -- 135 2637 0.3315 0.3764 -- 99.0
X Ray Diffraction 1.4452 1.4843 -- 133 2686 0.2943 0.3368 -- 100.0
X Ray Diffraction 1.4843 1.528 -- 154 2634 0.295 0.3629 -- 100.0
X Ray Diffraction 1.528 1.5773 -- 139 2668 0.2862 0.298 -- 100.0
X Ray Diffraction 1.5773 1.6337 -- 134 2707 0.2769 0.2907 -- 100.0
X Ray Diffraction 1.6337 1.6991 -- 135 2663 0.2691 0.2905 -- 100.0
X Ray Diffraction 1.6991 1.7765 -- 152 2689 0.2548 0.2737 -- 100.0
X Ray Diffraction 1.7765 1.8701 -- 151 2664 0.2605 0.3258 -- 100.0
X Ray Diffraction 1.8701 1.9873 -- 131 2685 0.2358 0.2679 -- 100.0
X Ray Diffraction 1.9873 2.1407 -- 141 2706 0.215 0.2566 -- 100.0
X Ray Diffraction 2.1407 2.3561 -- 164 2682 0.2007 0.2236 -- 100.0
X Ray Diffraction 2.3561 2.697 -- 142 2752 0.2135 0.2311 -- 100.0
X Ray Diffraction 2.697 3.3978 -- 155 2739 0.1935 0.2186 -- 100.0
X Ray Diffraction 3.3978 45.926 -- 131 2756 0.184 0.1844 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.5688
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.788
f_chiral_restr 0.066
f_bond_d 0.005
f_plane_restr 0.005
f_dihedral_angle_d 12.899
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1283
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 299

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10.1_2155
PDB_EXTRACT data extraction version: 3.20
d*TREK data reduction version: 9.9.9.10L
PHENIX model building
PHENIX phasing
d*TREK data scaling version: 9.9.9.10L