X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 298.0
Details Protein (10 mM Hepes pH 7.5, 100 mM NaCl + 5 mM Reduced glutathione), Reservoir (35 % v/v pentaerythritol ethoxylate (15/4 EO/OH) 0.2 M CaCl2, 0.1 M HEPES-NaOH pH 6.5), Cryoprotection (harvested straight from drop), VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.19 α = 90
b = 88.19 β = 90
c = 159.83 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE MIRRORS 2012-11-08
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-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
2.1 79.92 99.9 0.122 0.122 -- 15.2 22195 22195 0.0 0.0 36.77
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 2.21 100.0 0.76 0.76 1.0 15.5 3152

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 2.1 38.608 0.0 0.0 22054 22054 1123 99.5 0.2085 0.2085 0.2072 0.234 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 2.1 2.1956 -- 125 2534 0.2841 0.3249 -- 99.0
X Ray Diffraction 2.1956 2.3113 -- 147 2558 0.249 0.3045 -- 100.0
X Ray Diffraction 2.3113 2.4561 -- 139 2565 0.2291 0.3037 -- 100.0
X Ray Diffraction 2.4561 2.6457 -- 142 2566 0.2188 0.2698 -- 99.0
X Ray Diffraction 2.6457 2.9119 -- 138 2593 0.2116 0.2727 -- 100.0
X Ray Diffraction 2.9119 3.3331 -- 154 2615 0.2167 0.2413 -- 100.0
X Ray Diffraction 3.3331 4.1985 -- 132 2674 0.1868 0.2048 -- 100.0
X Ray Diffraction 4.1985 38.6142 -- 146 2826 0.1956 0.1989 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.6903
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.801
f_plane_restr 0.005
f_chiral_restr 0.071
f_angle_d 0.996
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1810
Nucleic Acid Atoms 0
Heterogen Atoms 41
Solvent Atoms 60

Software

Computing
Computing Package Purpose
UNKNOWN Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALA version: 3.3.20 data reduction