X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details 25 % polyethylene glycol 3350, 0.1 M BisTris, 0.25 M ammonium acetate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.13 α = 90
b = 70.13 β = 90
c = 62.33 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR scanner 345 mm plate -- 2010-08-16
Diffraction Radiation
Monochromator Protocol
Si 111 crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 0.9793, 0.9748, 0.9795 APS 22-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
1.65 50 98.9 0.069 -- -- 9.3 19139 19139 1.0 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)
1.65 1.71 100.0 0.422 -- -- 8.8 1892

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 1.65 46.589 -- 0.95 35544 19117 1808 99.3 -- 0.143 0.1401 0.1981 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 1.6491 1.6936 -- 142 2586 0.1426 0.2081 -- 100.0
X Ray Diffraction 1.6936 1.7435 -- 136 2643 0.1379 0.2104 -- 100.0
X Ray Diffraction 1.7435 1.7998 -- 152 2584 0.1235 0.2228 -- 100.0
X Ray Diffraction 1.7998 1.8641 -- 143 2593 0.116 0.186 -- 100.0
X Ray Diffraction 1.8641 1.9387 -- 129 2640 0.1171 0.1778 -- 100.0
X Ray Diffraction 1.9387 2.027 -- 147 2589 0.1167 0.2059 -- 100.0
X Ray Diffraction 2.027 2.1338 -- 161 2612 0.1135 0.1844 -- 100.0
X Ray Diffraction 2.1338 2.2675 -- 159 2566 0.1179 0.204 -- 100.0
X Ray Diffraction 2.2675 2.4426 -- 117 2622 0.1254 0.2288 -- 100.0
X Ray Diffraction 2.4426 2.6884 -- 134 2619 0.1439 0.208 -- 99.0
X Ray Diffraction 2.6884 3.0773 -- 135 2580 0.152 0.2157 -- 99.0
X Ray Diffraction 3.0773 3.8768 -- 141 2556 0.1387 0.1646 -- 98.0
X Ray Diffraction 3.8768 46.6072 -- 112 2546 0.1543 0.2024 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.361
Anisotropic B[1][1] 0.0337
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0337
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.0674
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.024
f_plane_restr 0.006
f_chiral_restr 0.078
f_angle_d 1.099
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1260
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 171

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.6_289) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
HKL data processing