X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 293.0
Details 100mM trisodium citrate-HCl, 1.3M ammonium sulfate, 210mM potassium sodium tartrate, 50mM imidazole, 400mM NaCl, 10mM MgCl2, 0.5mM 5'-O-[N-(L-seryl)sulfamoyl]adenosine, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 272.82 α = 90
b = 272.82 β = 90
c = 272.82 γ = 90
Symmetry
Space Group I 4 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
2 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 270 mirrors 2009-11-04
CCD ADSC QUANTUM 315r mirrors 2009-11-27
Diffraction Radiation
Monochromator Protocol
Si MAD
Si SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.07186, 1.07227, 1.05404 PHOTON FACTORY AR-NE3A
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.97848 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 50 99.9 0.094 0.094 -- 15.0 31746 31714 -- -2.0 102.66
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 3.21 100.0 0.847 0.847 3.49 14.6 3126

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 3.095 35.823 -- 1.33 31729 31040 1556 97.83 -- 0.2064 0.2036 0.2603 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 3.0954 3.1952 -- 135 2693 0.3066 0.3209 -- 100.0
X Ray Diffraction 3.1952 3.3094 -- 144 2671 0.2762 0.3422 -- 99.0
X Ray Diffraction 3.3094 3.4418 -- 152 2596 0.271 0.3792 -- 97.0
X Ray Diffraction 3.4418 3.5983 -- 126 2590 0.2478 0.3134 -- 95.0
X Ray Diffraction 3.5983 3.7878 -- 133 2617 0.2158 0.2572 -- 96.0
X Ray Diffraction 3.7878 4.0248 -- 158 2568 0.2009 0.2467 -- 96.0
X Ray Diffraction 4.0248 4.3351 -- 142 2635 0.1735 0.2337 -- 97.0
X Ray Diffraction 4.3351 4.7704 -- 118 2720 0.1619 0.2271 -- 99.0
X Ray Diffraction 4.7704 5.4586 -- 172 2715 0.1701 0.2255 -- 99.0
X Ray Diffraction 5.4586 6.8694 -- 139 2746 0.1984 0.2453 -- 99.0
X Ray Diffraction 6.8694 35.825 -- 137 2933 0.2108 0.2722 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 128.428
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.634
f_plane_restr 0.007
f_chiral_restr 0.082
f_angle_d 1.253
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4363
Nucleic Acid Atoms 2090
Heterogen Atoms 85
Solvent Atoms 0

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SHARP Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
SHARP model building
ADSC version: Quantum data collection