X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.4
Temperature 298.0
Details Protein Solution (40 mg/ml Ahp1 protein, in Milli-Q water containing 10mM DTT) mixed in a 1:1 ratio with the well solution (0.1 M BIS-TRIS pH 5.4, 2.0 M Ammonium Sulfate) Cryoprotected with 20% Glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 149.05 α = 90
b = 149.05 β = 90
c = 149.05 γ = 90
Symmetry
Space Group I 21 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 -- 2011-11-08
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.97915 SSRF BL17U

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 50 100.0 0.125 -- -- 44.8 37056 37056 0.0 0.0 29.79
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)
2.0 2.03 100.0 0.765 -- -- 45.0 1844

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 2.004 35.131 -- 1.33 37055 37007 1863 99.87 0.1584 0.1584 0.1576 0.1734 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 2.0036 2.0578 -- 138 2690 0.1862 0.2048 -- 100.0
X Ray Diffraction 2.0578 2.1183 -- 145 2686 0.1719 0.2169 -- 100.0
X Ray Diffraction 2.1183 2.1867 -- 140 2677 0.163 0.1859 -- 100.0
X Ray Diffraction 2.1867 2.2648 -- 143 2707 0.1652 0.2005 -- 100.0
X Ray Diffraction 2.2648 2.3555 -- 141 2676 0.1759 0.18 -- 100.0
X Ray Diffraction 2.3555 2.4626 -- 145 2666 0.1727 0.2006 -- 100.0
X Ray Diffraction 2.4626 2.5924 -- 141 2703 0.1726 0.242 -- 100.0
X Ray Diffraction 2.5924 2.7548 -- 143 2685 0.1744 0.2067 -- 100.0
X Ray Diffraction 2.7548 2.9674 -- 140 2689 0.1655 0.1664 -- 100.0
X Ray Diffraction 2.9674 3.2658 -- 148 2710 0.1591 0.1722 -- 100.0
X Ray Diffraction 3.2658 3.7379 -- 142 2721 0.1388 0.1448 -- 100.0
X Ray Diffraction 3.7379 4.7076 -- 147 2715 0.1261 0.139 -- 100.0
X Ray Diffraction 4.7076 35.1366 -- 150 2819 0.1714 0.1795 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.7781
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 11.438
f_plane_restr 0.004
f_chiral_restr 0.066
f_angle_d 0.907
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1422
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 246

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
PHENIX:PHASER Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction