X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 2 uL of protein solution(15-20 mg/ml, 50 mM TEA, pH 7.5, 100 mM KCL, 2 mM DTT, 10 mM deaza-PLP, 50 mM L-aspartate) mixed with 2 uL reservoir buffer (53-60% saturated ammonium sulfate and 50 mM TEA), VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 84.29 α = 90
b = 155.25 β = 90
c = 77.96 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2010-02-03
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 -- SSRL BL9-2

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
1.5 28.62 98.7 0.038 0.038 -- 4.24 81931 80890 0.0 -3.0 --
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)
1.5 1.54 93.9 0.543 0.543 2.03 2.73 --

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 1.5 28.617 -- 1.35 -- 80854 4061 98.74 -- 0.1704 0.1692 0.1935 --
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 1.5 1.5177 -- 111 2464 0.368 0.363 -- 92.0
X Ray Diffraction 1.5177 1.5362 -- 114 2510 0.3231 0.3203 -- 94.0
X Ray Diffraction 1.5362 1.5556 -- 118 2568 0.2975 0.2939 -- 95.0
X Ray Diffraction 1.5556 1.5761 -- 147 2610 0.265 0.286 -- 100.0
X Ray Diffraction 1.5761 1.5977 -- 156 2665 0.2551 0.291 -- 100.0
X Ray Diffraction 1.5977 1.6205 -- 134 2643 0.2426 0.3078 -- 100.0
X Ray Diffraction 1.6205 1.6447 -- 146 2646 0.2353 0.2549 -- 100.0
X Ray Diffraction 1.6447 1.6704 -- 147 2656 0.2078 0.2164 -- 100.0
X Ray Diffraction 1.6704 1.6978 -- 140 2649 0.2079 0.2482 -- 100.0
X Ray Diffraction 1.6978 1.727 -- 145 2653 0.2094 0.248 -- 100.0
X Ray Diffraction 1.727 1.7584 -- 141 2655 0.1984 0.2256 -- 100.0
X Ray Diffraction 1.7584 1.7922 -- 135 2659 0.1887 0.2448 -- 100.0
X Ray Diffraction 1.7922 1.8288 -- 126 2659 0.1842 0.2253 -- 99.0
X Ray Diffraction 1.8288 1.8686 -- 151 2648 0.1847 0.2454 -- 100.0
X Ray Diffraction 1.8686 1.912 -- 132 2647 0.1779 0.1841 -- 99.0
X Ray Diffraction 1.912 1.9598 -- 158 2629 0.1743 0.1949 -- 99.0
X Ray Diffraction 1.9598 2.0128 -- 148 2658 0.1733 0.2301 -- 99.0
X Ray Diffraction 2.0128 2.072 -- 150 2628 0.1671 0.2069 -- 99.0
X Ray Diffraction 2.072 2.1389 -- 147 2652 0.1587 0.2156 -- 99.0
X Ray Diffraction 2.1389 2.2153 -- 137 2672 0.162 0.173 -- 99.0
X Ray Diffraction 2.2153 2.304 -- 130 2625 0.1581 0.194 -- 98.0
X Ray Diffraction 2.304 2.4088 -- 136 2658 0.1632 0.203 -- 99.0
X Ray Diffraction 2.4088 2.5357 -- 143 2670 0.165 0.1816 -- 99.0
X Ray Diffraction 2.5357 2.6945 -- 183 2648 0.1667 0.2064 -- 100.0
X Ray Diffraction 2.6945 2.9023 -- 141 2705 0.1671 0.1787 -- 100.0
X Ray Diffraction 2.9023 3.194 -- 137 2705 0.1629 0.1848 -- 100.0
X Ray Diffraction 3.194 3.6554 -- 138 2730 0.1561 0.1764 -- 99.0
X Ray Diffraction 3.6554 4.6023 -- 133 2747 0.1361 0.1562 -- 99.0
X Ray Diffraction 4.6023 28.6218 -- 137 2734 0.1692 0.1724 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 1.3233
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.8079
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.5153
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.01
f_chiral_restr 0.115
f_dihedral_angle_d 12.866
f_angle_d 1.607
f_bond_d 0.016
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3065
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 447

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
MOLREP model building