X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.15
Details 6 % PEG 4000, 5 mM magnesium acetate and 50 mM ADA (pH 6.5)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.12 α = 90
b = 95.8 β = 90
c = 144.49 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 -- 2016-08-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID

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
2 35.68 99.9 0.116 -- -- 7.4 -- 50699 -- -- 27.72
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)
2.0 2.05 100.0 0.688 -- -- 7.4 --

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 2.0 14.742 -- 1.34 -- 50488 2462 99.89 -- 0.2182 0.2166 0.2513 --
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 2.0 2.0384 -- 128 2661 0.2747 0.2745 -- 100.0
X Ray Diffraction 2.0384 2.0799 -- 138 2593 0.2535 0.3036 -- 100.0
X Ray Diffraction 2.0799 2.125 -- 135 2656 0.249 0.263 -- 100.0
X Ray Diffraction 2.125 2.1743 -- 138 2623 0.2456 0.2764 -- 100.0
X Ray Diffraction 2.1743 2.2284 -- 149 2639 0.2421 0.2745 -- 100.0
X Ray Diffraction 2.2284 2.2885 -- 151 2623 0.2421 0.2855 -- 100.0
X Ray Diffraction 2.2885 2.3556 -- 140 2618 0.2287 0.2686 -- 100.0
X Ray Diffraction 2.3556 2.4313 -- 143 2652 0.2278 0.2934 -- 100.0
X Ray Diffraction 2.4313 2.5178 -- 151 2649 0.2229 0.2438 -- 100.0
X Ray Diffraction 2.5178 2.618 -- 116 2652 0.2184 0.2633 -- 100.0
X Ray Diffraction 2.618 2.7365 -- 116 2688 0.2313 0.2829 -- 100.0
X Ray Diffraction 2.7365 2.8797 -- 135 2656 0.2304 0.2789 -- 100.0
X Ray Diffraction 2.8797 3.0586 -- 125 2681 0.2289 0.2471 -- 100.0
X Ray Diffraction 3.0586 3.2924 -- 121 2702 0.2309 0.2677 -- 100.0
X Ray Diffraction 3.2924 3.6193 -- 133 2693 0.217 0.2606 -- 100.0
X Ray Diffraction 3.6193 4.1328 -- 143 2720 0.2002 0.2761 -- 100.0
X Ray Diffraction 4.1328 5.1694 -- 147 2721 0.1734 0.1706 -- 100.0
X Ray Diffraction 5.1694 14.7423 -- 153 2799 0.2 0.235 -- 98.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.003
f_dihedral_angle_d 17.124
f_chiral_restr 0.044
f_plane_restr 0.005
f_angle_d 0.705
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3937
Nucleic Acid Atoms 654
Heterogen Atoms 0
Solvent Atoms 265

Software

Software
Software Name Purpose
PHENIX refinement version: (1.11.1_2575: ???)
Aimless data scaling version: 0.5.1
PDB_EXTRACT data extraction version: 3.22
MOSFLM data reduction
MOLREP phasing