X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 291.0
Details 16-18% PEG 3350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.14 α = 90
b = 79.24 β = 106.69
c = 55.54 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 92 -- 2015-04-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 1.5418 -- --

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
2.1 50 95.9 0.073 -- -- 3.2 -- 22923 -- -- 40.45
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)
2.1 2.18 85.4 0.609 -- -- 2.7 --

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 2.097 20.846 -- 1.34 -- 22796 1988 95.2 -- 0.2228 0.2161 0.293 --
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 2.0975 2.1499 -- 116 1210 0.3028 0.3696 -- 77.0
X Ray Diffraction 2.1499 2.2079 -- 139 1457 0.2791 0.3525 -- 96.0
X Ray Diffraction 2.2079 2.2728 -- 145 1511 0.3032 0.3546 -- 97.0
X Ray Diffraction 2.2728 2.3461 -- 145 1513 0.2712 0.3882 -- 97.0
X Ray Diffraction 2.3461 2.4298 -- 141 1492 0.2625 0.3959 -- 97.0
X Ray Diffraction 2.4298 2.527 -- 142 1498 0.2781 0.3315 -- 96.0
X Ray Diffraction 2.527 2.6418 -- 144 1490 0.2931 0.3617 -- 96.0
X Ray Diffraction 2.6418 2.7807 -- 141 1477 0.3011 0.4108 -- 95.0
X Ray Diffraction 2.7807 2.9545 -- 137 1458 0.3098 0.4199 -- 93.0
X Ray Diffraction 2.9545 3.1819 -- 145 1508 0.2682 0.3666 -- 97.0
X Ray Diffraction 3.1819 3.5007 -- 150 1567 0.1976 0.2792 -- 99.0
X Ray Diffraction 3.5007 4.0042 -- 145 1522 0.1769 0.2411 -- 98.0
X Ray Diffraction 4.0042 5.0331 -- 147 1523 0.1685 0.2567 -- 96.0
X Ray Diffraction 5.0331 20.8469 -- 151 1582 0.1695 0.2109 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.076
f_angle_d 1.036
f_chiral_restr 0.053
f_plane_restr 0.008
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2614
Nucleic Acid Atoms 629
Heterogen Atoms 35
Solvent Atoms 120

Software

Software
Software Name Purpose
PHENIX refinement version: (1.10.1_2155)
HKL-2000 data reduction
HKL-2000 data scaling
PDB_EXTRACT data extraction version: 3.24
PHENIX phasing