X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 277.0
Details 85-90mM HEPES pH 7.5, 17-18% PEG4000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.9 α = 90
b = 68.57 β = 90
c = 110.5 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 -- 2015-11-23
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.00 APS 22-BM

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
1.65 50 100.0 0.063 -- 24.906 4.3 -- 55422 -- -- 19.4
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)
1.65 1.68 100.0 0.712 -- -- 4.3 --

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
-- 1.651 32.448 -- 1.35 -- 55352 2769 99.91 -- 0.1674 0.166 0.194 --
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 1.651 1.6795 -- 135 2554 0.2409 0.2694 0.0 99.0
X Ray Diffraction 1.6795 1.71 -- 137 2596 0.2269 0.2561 0.0 100.0
X Ray Diffraction 1.71 1.7429 -- 136 2595 0.2225 0.2385 0.0 100.0
X Ray Diffraction 1.7429 1.7785 -- 136 2579 0.2094 0.2513 0.0 100.0
X Ray Diffraction 1.7785 1.8172 -- 138 2620 0.1995 0.2377 0.0 100.0
X Ray Diffraction 1.8172 1.8594 -- 137 2605 0.1975 0.2513 0.0 100.0
X Ray Diffraction 1.8594 1.9059 -- 139 2586 0.1818 0.1844 0.0 100.0
X Ray Diffraction 1.9059 1.9574 -- 134 2607 0.1792 0.2157 0.0 100.0
X Ray Diffraction 1.9574 2.015 -- 134 2613 0.1752 0.1967 0.0 100.0
X Ray Diffraction 2.015 2.0801 -- 141 2628 0.1709 0.2227 0.0 100.0
X Ray Diffraction 2.0801 2.1544 -- 140 2584 0.1618 0.204 0.0 100.0
X Ray Diffraction 2.1544 2.2406 -- 135 2630 0.158 0.1876 0.0 100.0
X Ray Diffraction 2.2406 2.3426 -- 138 2618 0.1596 0.1943 0.0 100.0
X Ray Diffraction 2.3426 2.466 -- 142 2638 0.1537 0.1784 0.0 100.0
X Ray Diffraction 2.466 2.6205 -- 136 2625 0.157 0.1708 0.0 100.0
X Ray Diffraction 2.6205 2.8227 -- 138 2647 0.1623 0.1788 0.0 100.0
X Ray Diffraction 2.8227 3.1066 -- 140 2655 0.1702 0.1945 0.0 100.0
X Ray Diffraction 3.1066 3.5556 -- 141 2665 0.1513 0.162 0.0 100.0
X Ray Diffraction 3.5556 4.4778 -- 143 2708 0.1414 0.1638 0.0 100.0
X Ray Diffraction 4.4778 32.4541 -- 149 2830 0.172 0.2172 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.3037
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_bond_d 0.007
f_dihedral_angle_d 13.737
f_angle_d 0.96
f_chiral_restr 0.054
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2582
Nucleic Acid Atoms 364
Heterogen Atoms 75
Solvent Atoms 439

Software

Software
Software Name Purpose
PHENIX refinement version: 1.11.1_2575
HKL-2000 data collection
PDB_EXTRACT data extraction version: 3.20
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing