X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 277.0
Details 0.2 M MgCl2, 0.1 M Bis-Tris/HCl, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.09 α = 90
b = 67.09 β = 90
c = 109.87 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2012-08-01
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97931 APS 19-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
2.45 30 98.2 0.093 -- -- 4.7 10974 10779 -- -3.0 60.1
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)
2.45 2.49 99.8 0.763 -- 2.18 4.8 549

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
SAD 2.452 29.051 -- 0.0 10775 10775 810 98.22 0.1804 0.1804 0.1766 0.2257 random
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 2.452 2.6055 -- 135 1625 0.2431 0.2903 -- 98.0
X Ray Diffraction 2.6055 2.8065 -- 139 1645 0.248 0.3014 -- 99.0
X Ray Diffraction 2.8065 3.0887 -- 144 1637 0.2321 0.3128 -- 99.0
X Ray Diffraction 3.0887 3.5349 -- 138 1665 0.1934 0.2361 -- 99.0
X Ray Diffraction 3.5349 4.4511 -- 130 1670 0.1536 0.2383 -- 98.0
X Ray Diffraction 4.4511 29.0533 -- 124 1723 0.1492 0.1573 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.049
f_dihedral_angle_d 15.311
f_angle_d 0.853
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1802
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 11

Software

Computing
Computing Package Purpose
SBCcollect Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
SHELX, MLPHARE, DM, Buccaneer, ARP/WARP, COOT Structure Solution
PHENIX (phenix.refine: dev_1096) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: dev_1096) refinement
COOT model building
ARP/WARP model building
Buccaneer model building
DM model building
MLPHARE model building
SHELX model building
SBCcollect data collection