X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.9
Temperature 298.0
Details 1.5 uL of 13.2 mg/mL YjiA in 0.1 M NaCl, 25 mM HEPES, pH 7.6, mixed with 0.3 uL 0.1 M CaCl2 and 1.5 uL 1.55 M ammonium sulfate, 0.1 M , VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.29 α = 90
b = 68.87 β = 104.09
c = 77.83 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 MARMOSAIC 325 mm CCD -- 2007-07-21
Diffraction Radiation
Monochromator Protocol
Si(111) Double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 1.1808 SSRL BL9-2

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
2.57 30 97.0 -- 0.079 -- 3.8 35529 35529 -- -3.0 --
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)
2.57 2.61 84.6 -- 0.412 3.3 3.6 1535

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 2.57 29.126 -- 1.36 35283 35283 940 97.46 -- 0.2221 0.2199 0.2623 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 2.57 2.6395 -- 176 2619 0.3142 0.3748 -- 100.0
X Ray Diffraction 2.6395 2.7171 -- 152 2614 0.2796 0.3002 -- 100.0
X Ray Diffraction 2.7171 2.8047 -- 128 2674 0.2689 0.3238 -- 100.0
X Ray Diffraction 2.8047 2.9049 -- 103 2639 0.2748 0.3134 -- 100.0
X Ray Diffraction 2.9049 3.0211 -- 129 2670 0.2626 0.2971 -- 100.0
X Ray Diffraction 3.0211 3.1584 -- 124 2659 0.263 0.3299 -- 100.0
X Ray Diffraction 3.1584 3.3247 -- 138 2613 0.2456 0.3111 -- 100.0
X Ray Diffraction 3.3247 3.5327 -- 155 2638 0.2329 0.2219 -- 100.0
X Ray Diffraction 3.5327 3.8049 -- 106 1836 0.2437 0.3045 -- 70.0
X Ray Diffraction 3.8049 4.1868 -- 158 2603 0.2008 0.2608 -- 100.0
X Ray Diffraction 4.1868 4.7903 -- 129 2656 0.1606 0.2252 -- 100.0
X Ray Diffraction 4.7903 6.0265 -- 175 2619 0.1966 0.228 -- 100.0
X Ray Diffraction 6.0265 29.128 -- 131 2544 0.1956 0.222 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic with TLS
Mean Isotropic B 71.69
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.002
f_chiral_restr 0.039
f_dihedral_angle_d 9.79
f_angle_d 0.56
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4821
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 43

Software

Computing
Computing Package Purpose
Blu-ice Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.1_1168) refinement
Phaser model building
Blu-ice data collection