X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 298.0
Details Protein (10 mM Hepes pH 7.8, 150 mM NaCl, 5% glycerol, 1 mM EDTA/DTT); Reservoir (30% Peg300, MES pH 7.0, 200 mM MgCl); Cryoprotection (Reservoir+250 mM trans-4OH-L-Proline Betaine, comes with approx equal molar of iodine during synthesis of trans-4OH-L-Proline Betaine), temperature 298K, VAPOR DIFFUSION, SITTING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 117.46 α = 90
b = 117.46 β = 90
c = 111.05 γ = 90
Symmetry
Space Group P 4 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE MIRRORS 2012-07-09
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
1.7 111.05 99.9 0.104 0.104 -- 11.8 85566 85566 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)
1.7 1.79 99.8 0.773 0.773 1.0 8.3 12278

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
FOURIER SYNTHESIS 1.7 80.696 0.0 0.0 85473 85473 4275 99.82 0.1668 0.1668 0.1653 0.1966 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 1.7 1.7193 -- 135 2665 0.2408 0.3164 -- 100.0
X Ray Diffraction 1.7193 1.7396 -- 121 2687 0.2231 0.2707 -- 100.0
X Ray Diffraction 1.7396 1.7608 -- 137 2659 0.2136 0.2469 -- 100.0
X Ray Diffraction 1.7608 1.7831 -- 133 2674 0.2101 0.2412 -- 100.0
X Ray Diffraction 1.7831 1.8065 -- 131 2672 0.1986 0.2232 -- 100.0
X Ray Diffraction 1.8065 1.8313 -- 126 2673 0.187 0.2197 -- 100.0
X Ray Diffraction 1.8313 1.8574 -- 153 2662 0.188 0.2626 -- 100.0
X Ray Diffraction 1.8574 1.8852 -- 152 2669 0.1847 0.2188 -- 100.0
X Ray Diffraction 1.8852 1.9146 -- 121 2685 0.18 0.2112 -- 100.0
X Ray Diffraction 1.9146 1.946 -- 140 2694 0.1765 0.2447 -- 100.0
X Ray Diffraction 1.946 1.9796 -- 141 2675 0.1789 0.2094 -- 100.0
X Ray Diffraction 1.9796 2.0156 -- 140 2654 0.1682 0.2074 -- 100.0
X Ray Diffraction 2.0156 2.0544 -- 175 2670 0.166 0.2136 -- 100.0
X Ray Diffraction 2.0544 2.0963 -- 121 2722 0.1607 0.2113 -- 100.0
X Ray Diffraction 2.0963 2.1419 -- 148 2650 0.1667 0.2037 -- 100.0
X Ray Diffraction 2.1419 2.1917 -- 157 2683 0.1525 0.1891 -- 100.0
X Ray Diffraction 2.1917 2.2465 -- 161 2679 0.158 0.2153 -- 100.0
X Ray Diffraction 2.2465 2.3073 -- 131 2707 0.1546 0.1952 -- 100.0
X Ray Diffraction 2.3073 2.3752 -- 136 2695 0.1545 0.196 -- 100.0
X Ray Diffraction 2.3752 2.4518 -- 150 2697 0.1626 0.1967 -- 100.0
X Ray Diffraction 2.4518 2.5395 -- 145 2693 0.165 0.1946 -- 100.0
X Ray Diffraction 2.5395 2.6411 -- 130 2728 0.1557 0.1762 -- 100.0
X Ray Diffraction 2.6411 2.7613 -- 151 2699 0.1678 0.1977 -- 100.0
X Ray Diffraction 2.7613 2.9069 -- 162 2706 0.1699 0.2228 -- 100.0
X Ray Diffraction 2.9069 3.0891 -- 133 2756 0.1673 0.1859 -- 100.0
X Ray Diffraction 3.0891 3.3276 -- 143 2740 0.1533 0.1864 -- 100.0
X Ray Diffraction 3.3276 3.6625 -- 141 2757 0.1487 0.164 -- 100.0
X Ray Diffraction 3.6625 4.1924 -- 146 2787 0.1414 0.1587 -- 100.0
X Ray Diffraction 4.1924 5.2819 -- 144 2813 0.1446 0.1521 -- 100.0
X Ray Diffraction 5.2819 80.7868 -- 171 2947 0.1837 0.201 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.388
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.033
f_plane_restr 0.006
f_chiral_restr 0.068
f_angle_d 1.103
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5538
Nucleic Acid Atoms 0
Heterogen Atoms 54
Solvent Atoms 787

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHENIX 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