2ZXI

Structure of Aquifex aeolicus GidA in the form II crystal


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 293.0
Details 200mM ammonium chloride, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 119.41 α = 90
b = 98 β = 90
c = 129.62 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 270 mirrors 2008-06-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1 Photon Factory BL-17A

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
2.3 50 92.2 0.083 -- -- 3.7 -- 123831 -- -- --
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)
2.3 2.33 78.5 0.248 -- 2.0 2.5 --

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 2.3 19.92 -- 0.0 -- 122591 6095 92.4 -- 0.209 0.209 0.248 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 2.3 2.44 -- 889 17528 0.31 0.343 0.011 83.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 29.5
Anisotropic B[1][1] -6.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.24
Anisotropic B[2][2] -5.97
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 12.01
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.006
c_angle_deg 1.2
c_mcbond_it 1.75
c_scbond_it 3.07
c_scangle_it 4.37
c_improper_angle_d 0.83
c_mcangle_it 2.68
c_dihedral_angle_d 23.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.38
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.34
Luzzati Sigma A (R-Free Set) 0.41
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19268
Nucleic Acid Atoms 0
Heterogen Atoms 212
Solvent Atoms 1100

Software

Software
Software Name Purpose
CNS refinement version: 1.2
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing