X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 293.0
Details 16% PEG 4000, 0.08 M CH3COONA, 0.04 M, TRIS PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 34.54 α = 90.08
b = 70.96 β = 90.02
c = 78.26 γ = 90.29
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2009-04-02
Diffraction Radiation
Monochromator Protocol
SI (220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.000 APS 22-BM

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
1.96 25.9 94.6 -- 0.038 -- -- -- 49925 -- 5.0 19.46
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 2.04 94.7 -- 0.092 12.9 -- --

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 1.97 25.9 -- 0.06 -- 49480 1992 93.4 -- 0.166 0.165 0.198 --
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 1.965 2.014 -- 126 3168 0.185 0.249 -- 86.0
X Ray Diffraction 2.014 2.069 -- 143 3431 0.173 0.235 -- 94.0
X Ray Diffraction 2.069 2.129 -- 145 3416 0.176 0.225 -- 94.0
X Ray Diffraction 2.129 2.198 -- 142 3434 0.166 0.247 -- 95.0
X Ray Diffraction 2.198 2.277 -- 135 3429 0.183 0.252 -- 95.0
X Ray Diffraction 2.277 2.368 -- 146 3473 0.181 0.225 -- 95.0
X Ray Diffraction 2.368 2.475 -- 147 3486 0.184 0.238 -- 95.0
X Ray Diffraction 2.475 2.606 -- 145 3433 0.177 0.256 -- 95.0
X Ray Diffraction 2.606 2.769 -- 140 3414 0.18 0.207 -- 94.0
X Ray Diffraction 2.769 2.982 -- 147 3413 0.173 0.222 -- 95.0
X Ray Diffraction 2.982 3.282 -- 140 3399 0.162 0.19 -- 93.0
X Ray Diffraction 3.282 3.756 -- 139 3362 0.145 0.165 -- 92.0
X Ray Diffraction 3.756 4.727 -- 145 3327 0.134 0.147 -- 92.0
X Ray Diffraction 4.727 25.903 -- 152 3303 0.167 0.154 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.95
Anisotropic B[1][1] 11.486
Anisotropic B[1][2] 1.457
Anisotropic B[1][3] -2.512
Anisotropic B[2][2] -10.321
Anisotropic B[2][3] 0.631
Anisotropic B[3][3] -1.165
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.06
f_dihedral_angle_d 14.174
f_angle_d 0.892
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6783
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 628

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.005 data extraction
phenix refinement