X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 293.0
Details 1.65-1.68 M ammonium sulfate, 6.5-6.8% v/v 2-propanol, 0.1 M sodium citrate tribasic dihydrate pH 6.0 and 5 mM phenol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.54 α = 90
b = 107.29 β = 90
c = 157.57 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-06-22
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 1.0720 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 99.1 0.083 -- -- 8.3 72101 71457 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)
2.0 2.07 99.7 0.297 -- -- 8.3 7094

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 2.0 37.663 -- 1.34 72101 71392 3605 98.59 -- 0.1849 0.1828 0.2244 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 2.0 2.0266 -- 127 2213 0.1976 0.2823 -- 85.0
X Ray Diffraction 2.0266 2.0544 -- 124 2607 0.1998 0.2454 -- 100.0
X Ray Diffraction 2.0544 2.0837 -- 131 2612 0.1941 0.2612 -- 100.0
X Ray Diffraction 2.0837 2.1148 -- 147 2606 0.1882 0.2831 -- 100.0
X Ray Diffraction 2.1148 2.1479 -- 140 2601 0.1931 0.2383 -- 100.0
X Ray Diffraction 2.1479 2.1831 -- 137 2593 0.1853 0.2642 -- 100.0
X Ray Diffraction 2.1831 2.2207 -- 146 2615 0.1909 0.2489 -- 100.0
X Ray Diffraction 2.2207 2.2611 -- 155 2611 0.1832 0.2311 -- 100.0
X Ray Diffraction 2.2611 2.3046 -- 150 2587 0.1818 0.2402 -- 100.0
X Ray Diffraction 2.3046 2.3516 -- 151 2616 0.1868 0.2449 -- 100.0
X Ray Diffraction 2.3516 2.4027 -- 134 2634 0.1859 0.2352 -- 100.0
X Ray Diffraction 2.4027 2.4586 -- 138 2588 0.1911 0.2691 -- 100.0
X Ray Diffraction 2.4586 2.5201 -- 140 2618 0.1947 0.2555 -- 100.0
X Ray Diffraction 2.5201 2.5882 -- 131 2628 0.2064 0.2963 -- 100.0
X Ray Diffraction 2.5882 2.6644 -- 143 2616 0.1958 0.2515 -- 100.0
X Ray Diffraction 2.6644 2.7503 -- 135 2652 0.1985 0.2353 -- 100.0
X Ray Diffraction 2.7503 2.8486 -- 134 2624 0.2059 0.2392 -- 99.0
X Ray Diffraction 2.8486 2.9626 -- 157 2621 0.197 0.2609 -- 100.0
X Ray Diffraction 2.9626 3.0974 -- 128 2633 0.2016 0.2238 -- 99.0
X Ray Diffraction 3.0974 3.2606 -- 124 2650 0.191 0.2154 -- 99.0
X Ray Diffraction 3.2606 3.4648 -- 138 2641 0.1785 0.218 -- 99.0
X Ray Diffraction 3.4648 3.732 -- 142 2616 0.1708 0.2125 -- 99.0
X Ray Diffraction 3.732 4.1072 -- 141 2629 0.1587 0.1838 -- 98.0
X Ray Diffraction 4.1072 4.7006 -- 129 2634 0.1552 0.2 -- 97.0
X Ray Diffraction 4.7006 5.9185 -- 134 2635 0.177 0.1984 -- 96.0
X Ray Diffraction 5.9185 37.663 -- 149 2707 0.1864 0.1908 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.88
Anisotropic B[1][1] 2.1914
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.3433
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.5347
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.721
f_plane_restr 0.004
f_chiral_restr 0.07
f_angle_d 1.002
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7495
Nucleic Acid Atoms 481
Heterogen Atoms 58
Solvent Atoms 496

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASES Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction