X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.6
Temperature 283.15
Details Ammonium Sulafate, pH 8.6, VAPOR DIFFUSION, SITTING DROP, temperature 283.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.43 α = 111.11
b = 80.1 β = 90.1
c = 87.36 γ = 93.01
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 Rosenbaum-Rock Si (111) sagitally focused monochromator 2011-05-13
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock Si (111) sagitally focused monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 1.00004 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
2.7 50 93.0 0.074 -- -- 1.7 -- 43415 -- -- --
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)
2.703 2.77 84.7 0.317 -- -- 1.5 --

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 2.703 49.297 -- 0.06 -- 41120 1896 87.01 -- 0.2233 0.2208 0.2757 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 2.703 2.7706 -- 95 1844 0.3349 0.4473 -- 58.0
X Ray Diffraction 2.7706 2.8455 -- 108 2552 0.3068 0.3905 -- 78.0
X Ray Diffraction 2.8455 2.9292 -- 137 2594 0.2895 0.3528 -- 82.0
X Ray Diffraction 2.9292 3.0237 -- 133 2710 0.2702 0.3811 -- 85.0
X Ray Diffraction 3.0237 3.1318 -- 135 2870 0.2575 0.2834 -- 88.0
X Ray Diffraction 3.1318 3.2572 -- 134 2877 0.2323 0.3249 -- 89.0
X Ray Diffraction 3.2572 3.4054 -- 145 2869 0.2208 0.2743 -- 90.0
X Ray Diffraction 3.4054 3.5849 -- 143 2873 0.2106 0.2804 -- 90.0
X Ray Diffraction 3.5849 3.8094 -- 149 2946 0.2041 0.2579 -- 90.0
X Ray Diffraction 3.8094 4.1034 -- 137 2903 0.1942 0.234 -- 91.0
X Ray Diffraction 4.1034 4.5161 -- 139 2930 0.1764 0.2208 -- 91.0
X Ray Diffraction 4.5161 5.1689 -- 139 3011 0.185 0.2155 -- 94.0
X Ray Diffraction 5.1689 6.5099 -- 151 3114 0.2163 0.2847 -- 97.0
X Ray Diffraction 6.5099 49.3051 -- 151 3131 0.2381 0.2795 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 1.5001
Anisotropic B[1][2] -1.5437
Anisotropic B[1][3] -0.0816
Anisotropic B[2][2] 8.6507
Anisotropic B[2][3] 9.3194
Anisotropic B[3][3] -10.1508
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.079
f_dihedral_angle_d 18.418
f_angle_d 1.235
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11559
Nucleic Acid Atoms 0
Heterogen Atoms 384
Solvent Atoms 150

Software

Computing
Computing Package Purpose
EPICS Data Collection
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Phaser version: 2.3.0 molecular replacement
HKL data reduction