X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 5.6
Temperature 277.0
Details 100mM sodium citrate, 20% isopropanol, 20% PEG 4000 , pH 5.6, VAPOR DIFFUSION, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.31 α = 90
b = 75.37 β = 100.63
c = 35 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2010-11-11
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.0000 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
1.35 50 98.1 0.099 -- -- 3.5 35292 34621 1.0 1.0 --
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)
1.35 1.4 96.2 0.445 -- -- 2.9 --

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 1.35 30.055 -- 1.38 35292 34392 1756 97.14 -- 0.1323 0.1307 0.1614 --
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 1.35 1.3865 -- 121 2330 0.1777 0.2015 -- 91.0
X Ray Diffraction 1.3865 1.4273 -- 132 2426 0.1616 0.1947 -- 95.0
X Ray Diffraction 1.4273 1.4734 -- 156 2482 0.1401 0.1856 -- 97.0
X Ray Diffraction 1.4734 1.5261 -- 141 2511 0.1336 0.1658 -- 97.0
X Ray Diffraction 1.5261 1.5872 -- 123 2551 0.1112 0.15 -- 97.0
X Ray Diffraction 1.5872 1.6594 -- 130 2497 0.1082 0.1452 -- 98.0
X Ray Diffraction 1.6594 1.7469 -- 143 2545 0.1064 0.1397 -- 99.0
X Ray Diffraction 1.7469 1.8563 -- 115 2577 0.1073 0.1419 -- 99.0
X Ray Diffraction 1.8563 1.9996 -- 152 2522 0.103 0.1327 -- 99.0
X Ray Diffraction 1.9996 2.2008 -- 149 2576 0.1025 0.1278 -- 99.0
X Ray Diffraction 2.2008 2.5191 -- 136 2589 0.1181 0.1466 -- 100.0
X Ray Diffraction 2.5191 3.1732 -- 146 2593 0.1409 0.1912 -- 100.0
X Ray Diffraction 3.1732 30.0628 -- 112 2437 0.1564 0.1744 -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.6861
Anisotropic B[1][1] 0.3295
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.441
Anisotropic B[2][2] -1.58
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.2505
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.01
f_chiral_restr 0.109
f_dihedral_angle_d 13.268
f_angle_d 1.713
f_bond_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1149
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 235

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction
DENZO data collection