X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.8
Temperature 293.0
Details 1.6 M sodium citrate, 50 mM Tris-HCl pH 7.8

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.18 α = 90
b = 41.34 β = 104.12
c = 71.82 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
IMAGE PLATE RIGAKU RAXIS IV++ -- 2015-03-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 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
1.5 50 98.1 0.047 -- 47.194 3.3 -- 38042 -- -- 20.17
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)
1.5 1.53 98.1 0.321 -- -- 3.0 1885

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 1.5 32.024 -- 1.34 -- 38025 1902 97.87 -- 0.1563 0.1553 0.1733 random selection
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 1.5 1.5355 -- 117 2481 0.2262 0.2722 -- 95.0
X Ray Diffraction 1.5355 1.577 -- 141 2523 0.2046 0.2347 -- 97.0
X Ray Diffraction 1.577 1.6234 -- 136 2551 0.2128 0.2605 -- 96.0
X Ray Diffraction 1.6234 1.6758 -- 132 2504 0.187 0.1989 -- 96.0
X Ray Diffraction 1.6758 1.7357 -- 142 2496 0.1574 0.1848 -- 95.0
X Ray Diffraction 1.7357 1.8052 -- 123 2536 0.1576 0.2104 -- 96.0
X Ray Diffraction 1.8052 1.8874 -- 145 2566 0.1531 0.1933 -- 98.0
X Ray Diffraction 1.8874 1.9869 -- 130 2592 0.1526 0.1804 -- 99.0
X Ray Diffraction 1.9869 2.1113 -- 135 2650 0.1461 0.1846 -- 99.0
X Ray Diffraction 2.1113 2.2743 -- 139 2591 0.1517 0.1717 -- 99.0
X Ray Diffraction 2.2743 2.5031 -- 138 2638 0.15 0.156 -- 100.0
X Ray Diffraction 2.5031 2.8651 -- 140 2637 0.1613 0.1715 -- 100.0
X Ray Diffraction 2.8651 3.609 -- 143 2662 0.1493 0.1661 -- 100.0
X Ray Diffraction 3.609 4.0 -- 141 2696 0.146 0.1556 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.1905
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.006
f_dihedral_angle_d 13.435
f_angle_d 1.324
f_chiral_restr 0.048
f_plane_restr 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2049
Nucleic Acid Atoms 0
Heterogen Atoms 38
Solvent Atoms 285

Software

Software
Software Name Purpose
HKL-2000 data collection
HKL-2000 data scaling
PHENIX refinement
PDB_EXTRACT data extraction version: 3.15
HKL-2000 data reduction
PHENIX phasing