X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Sitting Drop Vapor Diffusion
pH 7
Temperature 298.0
Details Protein (10 mM Hepes pH 7.5, 25 mM NaCl, 5 mM Reduced glutathione), Reservoir (25% Sokalan CP7, 0.1 M KCl, 0.1 M HEPES pH 7), Cryoprotection (reservoir + 20% glycerol), sitting drop vapor diffusion, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56 α = 90
b = 196.34 β = 90
c = 275.36 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 MIRRORS 2012-08-13
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
2.65 275.36 98.5 0.095 0.095 -- 15.0 43996 43996 0.0 0.0 --
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)
2.65 2.79 98.2 0.869 0.869 0.9 15.3 6328

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 2.65 92.47 0.0 0.0 43896 43896 2228 97.94 0.201 0.201 0.1981 0.2543 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 2.65 2.7076 -- 128 2553 0.261 0.326 -- 98.0
X Ray Diffraction 2.7076 2.7706 -- 143 2566 0.245 0.3342 -- 98.0
X Ray Diffraction 2.7706 2.8399 -- 123 2578 0.2312 0.258 -- 97.0
X Ray Diffraction 2.8399 2.9167 -- 132 2568 0.2253 0.2814 -- 98.0
X Ray Diffraction 2.9167 3.0025 -- 126 2597 0.2257 0.3283 -- 98.0
X Ray Diffraction 3.0025 3.0994 -- 146 2566 0.2085 0.3007 -- 97.0
X Ray Diffraction 3.0994 3.2101 -- 133 2525 0.2078 0.2658 -- 98.0
X Ray Diffraction 3.2101 3.3386 -- 141 2602 0.2113 0.2714 -- 98.0
X Ray Diffraction 3.3386 3.4905 -- 156 2611 0.1932 0.3221 -- 98.0
X Ray Diffraction 3.4905 3.6744 -- 135 2575 0.178 0.2352 -- 98.0
X Ray Diffraction 3.6744 3.9045 -- 151 2598 0.1746 0.24 -- 98.0
X Ray Diffraction 3.9045 4.2058 -- 145 2602 0.1705 0.2113 -- 98.0
X Ray Diffraction 4.2058 4.6287 -- 154 2652 0.1602 0.2187 -- 99.0
X Ray Diffraction 4.6287 5.2977 -- 133 2640 0.1805 0.2232 -- 99.0
X Ray Diffraction 5.2977 6.6713 -- 129 2706 0.2138 0.2415 -- 99.0
X Ray Diffraction 6.6713 46.235 -- 153 2729 0.2257 0.2653 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 61.9006
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.117
f_plane_restr 0.005
f_chiral_restr 0.067
f_angle_d 1.074
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7209
Nucleic Acid Atoms 0
Heterogen Atoms 100
Solvent Atoms 86

Software

Computing
Computing Package Purpose
UNKNOWN Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
BALBES 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