X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.55
Temperature 293.0
Details 10% PEG6000, 4% glucose, 2% ethylene glycol, 0.1 M tri-potassium citrate, 0.01% azide, pH 5.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.31 α = 76.18
b = 88.25 β = 69.29
c = 106.42 γ = 66.69
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD NOIR-1 -- 2010-09-10
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock monochromator 1: high-resolution double crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 0.97909 ALS 4.2.2

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
3 50 87.9 0.164 -- -- 4.1 47950 47882 -- -3.0 70.46
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)
3.0 3.19 84.9 0.622 -- 2.55 4.2 7714

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
SAD, MOLECULAR REPLACEMENT 3.0 49.36 1.96 1.96 47950 47882 2394 87.16 -- 0.2307 0.2295 0.253 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 3.0 3.0613 2244 122 2244 0.3506 0.3887 -- 73.0
X Ray Diffraction 3.0613 3.1279 2613 139 2613 0.3198 0.3255 -- 85.0
X Ray Diffraction 3.1279 3.2006 2631 138 2631 0.2895 0.3703 -- 85.0
X Ray Diffraction 3.2006 3.2806 2607 136 2607 0.2817 0.3207 -- 84.0
X Ray Diffraction 3.2806 3.3693 2531 134 2531 0.2681 0.2884 -- 84.0
X Ray Diffraction 3.3693 3.4685 2552 133 2552 0.2877 0.3478 -- 83.0
X Ray Diffraction 3.4685 3.5804 2568 136 2568 0.2725 0.28 -- 83.0
X Ray Diffraction 3.5804 3.7083 2540 134 2540 0.2963 0.2798 -- 83.0
X Ray Diffraction 3.7083 3.8567 2526 131 2526 0.2497 0.2901 -- 83.0
X Ray Diffraction 3.8567 4.0322 2518 134 2518 0.2573 0.2761 -- 82.0
X Ray Diffraction 4.0322 4.2446 2586 137 2586 0.2139 0.2506 -- 84.0
X Ray Diffraction 4.2446 4.5104 2638 135 2638 0.1982 0.2189 -- 86.0
X Ray Diffraction 4.5104 4.8584 2810 149 2810 0.19 0.1928 -- 91.0
X Ray Diffraction 4.8584 5.3468 2955 154 2955 0.1944 0.2236 -- 97.0
X Ray Diffraction 5.3468 6.1192 3049 161 3049 0.2095 0.2417 -- 99.0
X Ray Diffraction 6.1192 7.7049 3054 161 3054 0.2111 0.2519 -- 100.0
X Ray Diffraction 7.7049 49.3669 3066 160 3066 0.1968 0.2051 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 83.3211
Anisotropic B[1][1] -3.3931
Anisotropic B[1][2] 1.0886
Anisotropic B[1][3] 4.4702
Anisotropic B[2][2] -3.7601
Anisotropic B[2][3] 4.2764
Anisotropic B[3][3] 7.1532
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 9.662
f_plane_restr 0.002
f_chiral_restr 0.041
f_angle_d 0.538
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 18588
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 72

Software

Computing
Computing Package Purpose
BLUE ICE Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SOLVE, PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
RESOLVE density modification
SOLVE phasing
Phaser molecular replacement
HKL data reduction