X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details 120mM Tris-HCl, 11% PEG 4000, 400mM CaCl2, 160mM KCl, 5.0mM NiCl2, 50mM Na2S2O3, 50mM L-serine, 0.2M NaCl, 10mM 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.82 α = 90
b = 280.94 β = 113.45
c = 97.64 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
2 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2008-02-19
CCD ADSC QUANTUM 270 mirrors 2008-03-04
Diffraction Radiation
Monochromator Protocol
Si MAD
Si SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.97917, 0.97947 SPRING-8 BL41XU
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.07117 PHOTON FACTORY BL-17A

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
3.19 50 99.5 0.09 0.09 -- 7.4 75523 75145 -- -2.0 --
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)
3.2 3.31 96.0 0.674 0.674 2.5 6.2 7513

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
MAD 3.192 48.941 -- 1.35 75789 75046 3750 99.02 -- 0.1769 0.1738 0.2354 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 3.1925 3.2329 -- 105 2173 0.2771 0.3679 -- 82.0
X Ray Diffraction 3.2329 3.2754 -- 150 2554 0.272 0.3376 -- 96.0
X Ray Diffraction 3.2754 3.3202 -- 148 2623 0.2803 0.3303 -- 99.0
X Ray Diffraction 3.3202 3.3677 -- 122 2707 0.2634 0.3644 -- 100.0
X Ray Diffraction 3.3677 3.4179 -- 153 2567 0.2588 0.3128 -- 100.0
X Ray Diffraction 3.4179 3.4713 -- 139 2726 0.2327 0.2863 -- 100.0
X Ray Diffraction 3.4713 3.5282 -- 136 2620 0.231 0.3236 -- 100.0
X Ray Diffraction 3.5282 3.589 -- 142 2689 0.23 0.3083 -- 100.0
X Ray Diffraction 3.589 3.6543 -- 136 2621 0.2164 0.2576 -- 100.0
X Ray Diffraction 3.6543 3.7245 -- 137 2709 0.2163 0.3154 -- 100.0
X Ray Diffraction 3.7245 3.8005 -- 121 2650 0.2027 0.305 -- 100.0
X Ray Diffraction 3.8005 3.8831 -- 164 2667 0.1874 0.2548 -- 100.0
X Ray Diffraction 3.8831 3.9734 -- 142 2622 0.1783 0.2307 -- 100.0
X Ray Diffraction 3.9734 4.0728 -- 138 2726 0.1693 0.2456 -- 100.0
X Ray Diffraction 4.0728 4.1828 -- 149 2632 0.1687 0.2374 -- 100.0
X Ray Diffraction 4.1828 4.3058 -- 148 2623 0.1648 0.2453 -- 100.0
X Ray Diffraction 4.3058 4.4447 -- 137 2684 0.1388 0.1876 -- 100.0
X Ray Diffraction 4.4447 4.6035 -- 148 2641 0.1287 0.1847 -- 100.0
X Ray Diffraction 4.6035 4.7876 -- 135 2671 0.1195 0.1764 -- 100.0
X Ray Diffraction 4.7876 5.0053 -- 131 2686 0.1354 0.1974 -- 100.0
X Ray Diffraction 5.0053 5.2689 -- 133 2669 0.1492 0.2267 -- 100.0
X Ray Diffraction 5.2689 5.5986 -- 126 2680 0.1665 0.2385 -- 100.0
X Ray Diffraction 5.5986 6.0302 -- 137 2675 0.2011 0.2406 -- 100.0
X Ray Diffraction 6.0302 6.6357 -- 153 2693 0.2014 0.2917 -- 100.0
X Ray Diffraction 6.6357 7.5928 -- 137 2664 0.1666 0.2291 -- 100.0
X Ray Diffraction 7.5928 9.5544 -- 148 2678 0.1263 0.1781 -- 100.0
X Ray Diffraction 9.5544 48.947 -- 135 2646 0.1756 0.2104 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 130.118
Anisotropic B[1][1] -21.7714
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -6.6801
Anisotropic B[2][2] -9.6703
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 31.4417
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.459
f_plane_restr 0.004
f_chiral_restr 0.071
f_angle_d 1.22
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 30712
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 0

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
autoSHARP Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
DM density modification
HKL data reduction