X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 290.0
Details EB Synergy screen c10: 40% iso-propanol, 15% PEG 8000, 100mM imidazole/HCl, EhchA.00496.a.A1.PB00060 at 21mg/ml, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 87.49 α = 90
b = 32.58 β = 119.65
c = 89.08 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 ADSC QUANTUM 315r -- 2012-05-12
Diffraction Radiation
Monochromator Protocol
Single crystal, cylindrically bent, Si(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.1 0.977408 ALS 5.0.1

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
2.55 20 99.1 0.114 -- -- 3.7 14800 14664 0.0 -3.0 35.579
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)
2.55 2.62 99.4 0.489 -- 2.76 -- --

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 2.55 19.355 0.0 1.36 14800 14656 740 99.69 -- 0.171 0.1684 0.219 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 2.55 2.7464 -- 143 2742 0.2096 0.2987 -- 100.0
X Ray Diffraction 2.7464 3.0219 -- 156 2740 0.2018 0.2626 -- 100.0
X Ray Diffraction 3.0219 3.457 -- 139 2772 0.1811 0.2509 -- 100.0
X Ray Diffraction 3.457 4.3473 -- 150 2776 0.148 0.1852 -- 100.0
X Ray Diffraction 4.3473 19.3552 -- 152 2886 0.1503 0.1872 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic, TLS
Mean Isotropic B 21.7883
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.165
f_plane_restr 0.005
f_chiral_restr 0.043
f_angle_d 1.044
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2480
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 72

Software

Computing
Computing Package Purpose
BOS Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: dev_1269) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser version: 2.5.1 molecular replacement
Xscale data reduction