X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details 11% PEG 8000, 50 mM BisTris-propane pH 7.0, 50 mM NaCl, 5 mM HEPES pH 7.0, 0.3 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.68 α = 90
b = 77.7 β = 90
c = 121.3 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 MARMOSAIC 300 mm CCD -- 2009-08-05
Diffraction Radiation
Monochromator Protocol
Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 0.9686, 0.97947 APS 23-ID-D

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
1.97 50 97.9 0.101 -- -- 13.6 -- 43894 -- -- --
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)
1.97 2.0 82.7 0.566 -- -- 8.8 1813

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
MAD 1.975 36.999 -- 1.33 -- 43791 2185 97.41 -- 0.192 0.192 0.206 --
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 1.975 2.018 -- 103 2073 0.24 0.252 -- 79.0
X Ray Diffraction 2.018 2.065 -- 125 2318 0.238 0.244 -- 88.0
X Ray Diffraction 2.065 2.117 -- 140 2473 0.234 0.252 -- 95.0
X Ray Diffraction 2.117 2.174 -- 134 2592 0.218 0.229 -- 98.0
X Ray Diffraction 2.174 2.238 -- 130 2621 0.199 0.217 -- 100.0
X Ray Diffraction 2.238 2.31 -- 145 2626 0.199 0.213 -- 100.0
X Ray Diffraction 2.31 2.392 -- 139 2633 0.201 0.211 -- 100.0
X Ray Diffraction 2.392 2.488 -- 119 2674 0.193 0.204 -- 100.0
X Ray Diffraction 2.488 2.602 -- 147 2633 0.192 0.215 -- 100.0
X Ray Diffraction 2.602 2.739 -- 122 2672 0.2 0.229 -- 100.0
X Ray Diffraction 2.739 2.91 -- 158 2640 0.204 0.222 -- 100.0
X Ray Diffraction 2.91 3.135 -- 125 2692 0.204 0.241 -- 100.0
X Ray Diffraction 3.135 3.45 -- 133 2693 0.188 0.194 -- 100.0
X Ray Diffraction 3.45 3.949 -- 160 2691 0.174 0.199 -- 100.0
X Ray Diffraction 3.949 4.973 -- 146 2731 0.141 0.163 -- 100.0
X Ray Diffraction 4.973 37.005 -- 159 2844 0.19 0.178 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.544
Anisotropic B[1][1] -2.544
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.8
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.344
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.797
f_bond_d 0.019
f_angle_d 1.352
f_plane_restr 0.005
f_chiral_restr 0.102
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3684
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 258

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SHARP phasing
DM phasing version: 5.0
PHENIX refinement version: 1.5_2
PDB_EXTRACT data extraction version: 3.005
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling