X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8
Temperature 297.0
Details 100mM imidazole, 35% 2-methyl-2,4-pentanediol, 200mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.17 α = 90
b = 179.07 β = 102.53
c = 109.36 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210r -- 2005-11-23
Diffraction Radiation
Monochromator Protocol
SI 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A -- PHOTON FACTORY BL-5A

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
3.1 30 98.5 0.066 -- -- -- -- 39532 -- -- 57.7
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)
3.1 3.15 85.5 0.23 -- -- -- --

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 3.1 29.84 -- 1.38 -- 39493 1983 98.2 -- 0.187 0.185 0.227 --
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 3.1001 3.1775 -- 129 2246 0.2803 0.3533 -- 83.0
X Ray Diffraction 3.1775 3.2634 -- 131 2554 0.2575 0.3334 -- 94.0
X Ray Diffraction 3.2634 3.3593 -- 126 2674 0.2147 0.3009 -- 98.0
X Ray Diffraction 3.3593 3.4675 -- 143 2736 0.2173 0.266 -- 100.0
X Ray Diffraction 3.4675 3.5913 -- 147 2664 0.2103 0.2604 -- 100.0
X Ray Diffraction 3.5913 3.7348 -- 140 2767 0.2049 0.2853 -- 100.0
X Ray Diffraction 3.7348 3.9044 -- 131 2745 0.1759 0.1992 -- 100.0
X Ray Diffraction 3.9044 4.1098 -- 125 2729 0.1643 0.2235 -- 100.0
X Ray Diffraction 4.1098 4.3665 -- 157 2707 0.1529 0.1667 -- 100.0
X Ray Diffraction 4.3665 4.7025 -- 122 2755 0.1462 0.1827 -- 100.0
X Ray Diffraction 4.7025 5.1735 -- 164 2704 0.1736 0.2116 -- 100.0
X Ray Diffraction 5.1735 5.917 -- 163 2743 0.2092 0.2488 -- 100.0
X Ray Diffraction 5.917 7.4357 -- 164 2711 0.1951 0.2188 -- 100.0
X Ray Diffraction 7.4357 29.8455 -- 141 2775 0.1531 0.1775 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 54.21
Anisotropic B[1][1] 11.4589
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 7.469
Anisotropic B[2][2] -19.2139
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 7.7549
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.009
f_chiral_restr 0.131
f_dihedral_angle_d 17.814
f_angle_d 1.632
f_bond_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 15119
Nucleic Acid Atoms 0
Heterogen Atoms 78
Solvent Atoms 72

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS Structure Solution
PHENIX (PHENIX.REFINE: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement