X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 1.5 uL of 12.4 mg/mL triple mutant YjiA in 0.1 M NaCl, 1 mM TCEP, 25 mM HEPES, mixed with 0.3 uL 0.1 M CaCl2 and 1.5 uL 1.3 M ammonium sulfate, 0.1 M HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.07 α = 90
b = 68.44 β = 104.23
c = 77.7 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
PIXEL PSI PILATUS 6M -- 2012-07-15
Diffraction Radiation
Monochromator Protocol
Si(111) cryo-cooled double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.9795 APS 24-ID-C

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
2.05 75.3 98.5 -- 0.085 -- 6.5 35715 35715 -- -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)
2.05 2.09 98.8 -- 0.59 2.9 5.7 1784

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 2.05 75.3 -- 1.38 35309 35309 1747 98.31 -- 0.2044 0.2027 0.2381 same as for Zn(II)-soaked WT YjiA between 30 and 2.57 A resolution, random for remainder
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 2.05 2.1103 -- 140 2790 0.2556 0.2964 -- 99.0
X Ray Diffraction 2.1103 2.1785 -- 136 2787 0.2477 0.3248 -- 99.0
X Ray Diffraction 2.1785 2.2563 -- 146 2822 0.2385 0.2847 -- 99.0
X Ray Diffraction 2.2563 2.3467 -- 133 2779 0.2259 0.2684 -- 97.0
X Ray Diffraction 2.3467 2.4535 -- 150 2787 0.2347 0.2604 -- 99.0
X Ray Diffraction 2.4535 2.5828 -- 145 2797 0.2219 0.2691 -- 99.0
X Ray Diffraction 2.5828 2.7447 -- 165 2768 0.2151 0.2498 -- 98.0
X Ray Diffraction 2.7447 2.9566 -- 122 2806 0.2224 0.2491 -- 98.0
X Ray Diffraction 2.9566 3.2541 -- 136 2813 0.209 0.2422 -- 99.0
X Ray Diffraction 3.2541 3.725 -- 160 2775 0.1804 0.2052 -- 98.0
X Ray Diffraction 3.725 4.693 -- 160 2835 0.165 0.215 -- 99.0
X Ray Diffraction 4.693 75.3651 -- 154 2803 0.1984 0.2214 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic with TLS
Mean Isotropic B 43.79
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.049
f_dihedral_angle_d 11.38
f_angle_d 0.727
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4811
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 256

Software

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